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Lewis and Crosetti uncover a woman who's been killing her husbands for insurance money. Howard tries to keep her cases-solved record perfect, but she is reassigned with Felton as her partner. Bolander convinces Munch to help him finish up an unsolved case. A new guy, Tim Bayliss, from the mayor's office gets his first case in homicide, the murder of an 11-year-old girl. His partner Pembleton, we find out, is less than enthusiastic to work with him or anyone else in the unit.
Bayliss and Pembleton continue to struggle with the Watson case. Bolander and Munch discuss "iguana style" and are called to check out the homicide of a victim that isn't dead, at least the first time they're called. While checking out some leads for the Watson case, Crosetti gives his theory on the conspiracy to kill Abraham Lincoln. Lewis wants to flood Memorial Stadium. Bolander expresses an interest in Dr. Blythe; Munch advises and sends flower's in Stan's name. Danvers needs a stronger case; however, Howard is frustrated with a dead end. Then the ghost of the victim leads her to the undiscovered proof. Tim attends Adena's funeral.
Crosetti lays out more theories on his Lincoln assassination conspiracy theory. Then Gee comes in with news that Crosetti's friend Chris Thormann has been shot. After they follow up on a new lead in the case that takes them nowhere, frustration begins to set in for Bayliss. Bolander meets his neighbor, a man who works with wood. One of his projects is a coffin. Together, they drink Stan's beer and discuss life, love, and etc.. Kay and Beau's suspect in a murder hired a hit man to kill a man she disagreed with about a bust of Spiro Agnew. Their case leads to a solution for Meldrick's case involving the "black widow." Crosetti demands that he get the case to solve Chris' shooting. Stan meets Carol for their first date; however, they get interrupted when his neighbor is found dead. Gee talks with Bayliss about his frustration. Chris is going to survive, but what level he will recover to is yet to be determined.
Bolander and Munch tackle a case, but Stan keeps throwing his old partner's name at John. Evidently the date with Carol didn't go that well, he doesn't want to talk to her or about her. Pembleton (with Felton) and Bayliss follow different hunches in the Watson case. Chris' recovery is amazing, but it will take a lot of therapy and his getting used to being blind. The suspect in Chris' shooting gives himself up, to prevent being the victim of police justice. Lewis isn't as sure as Crosetti that their suspect is the one. Barnfather lets out a key piece of evidence to the media, taking the wind out of Tim's line of questioning for his suspect. Tim lets him know how he feels, and even though he is right, he must apologize. Pembleton and Felton discuss various racial issues while following up their lead. Carol finally catches up with Stan. Munch wants nothing to do with Karaoke at the bar, but finally gives in and enjoys himself. Frank gets hold of evidence that will allow them to follow up on Tim's lead.
Pembleton and Bayliss have only twelve hours to grill their prime suspect in the Adena Watson case before they must let him go.
Gee must help an old friend get used to his retirement. In their first case following the unsolved Adena Watson case, Bayliss and Pembleton check out the death of a police dog. Howard and Felton track down a drug dealer that is wanted for a torture / murder. Crosetti continues to help Chris deal with his recovery and finds out his wife is pregnant. Bolander meets Carol's son who later accompanies him to a crime scene.
A Chinese political refugee is murdered. Bolander and Munch investigate a murder of a man whose body is found in the park. Lewis and Crosetti go to the Chinese Embassy in Washington while looking into the murder of the Chinese political refugee. After they leave, a U.S. government official tells them to back off. Gee is looking for Pembleton because Pembleton may be up for a promotion. Howard nearly botches her testimony against the drug dealer. Pembleton is up for a promotion that he may not want.
The building is checked for air quality and later Gee is outraged when the asbestos removal teams come in without his knowledge. While investigating the death of a gang member, Bolander and Munch use an "Electrolyte-Neutron Magnetic Test" to break a boy into giving up the guilty party. Felton and Pembleton can't understand why their partners are trying to quit smoking, again.
On a slow and hot September night in the squad room with no air conditioning, the detectives spend the night together. Bayliss has a new suspect brought in on the Adena Watson case, a twelve-year-old boy. Munch deals with his breakup of his latest relationship. There is a mystery about a solitary lit candle in the squad room: who lights it and why? Bolander debates about calling the Dr. Blythe for a date. Santa Claus drops by depressed about today's society. Gee finds an abandoned baby in basement of the building.
All the detectives scramble to solve the case, when the mother, in a family on vacation, is murdered during a holdup. The husband has a hard time dealing with the reality of him not doing anything during the situation and Felton's indifference. When the suspects are found Howard is convinced that the youth who confesses to the murder didn't do it.
Gee informs the detectives that they must meet with a sensitivity consultant. Felton protects a friend who's going to help his terminally ill father commit suicide. Pembleton investigates a routine murder that escalates into a case of possible police brutality. Bolander has no intention of meeting with the consultant to the point where he takes a suspension without pay. Lewis investigates the death of the father of Felton's friend and discovers the truth and confronts Beau.
Things begin to heat up between Pembleton and Gee over the alleged police brutality case and one of the suspects is an ex-lover of Kay's. Bolander meets a waitress who encourages him to resume his cello playing. Munch's girlfriend is less than enthusiastic when he surprises her with a new fish for her tank. Frank, in the box, gets the confession that Gee is looking for. Unfortunately, the suspect is anything but guilty of that crime.
Bolander asks Kay if she would double date with him and Linda, to try to take the pressure off his first real date. A slain phone-sex operator is found clutching a note naming her boss as the perpetrator, Bayliss and Pembleton investigate. Munch has trouble dealing with Bolander's happiness, so he crashes the double date and makes everyone miserable. A man is shot to death over a pen at the library, Lewis and Crosetti investigate and find a man with a pen fetish. As Bayliss looks into the murder he begins to get involved.
When the winner of the city's Good Samaritan Award is murdered, Gee and his staff are called to help the new female night shift commander. Pembleton is at odds with the detective he shares a desk with. Beau and his wife separate and Kay gets caught in the middle. Meldrick and Munch have plans to buy a bar and try to persuade Bolander to also become a partner. Bayliss agrees to become a "silent" partner. In passing, Crosetti is said to be in Atlantic City on a "shots, slots and sluts" dream vacation.
Gaffney allows a possible murder site to be washed down which causes Pembleton to go off on him. Russert takes Gaffney off the case and Pembleton is made the primary. Things get more complicated as a second victim is found. Beau tries to decide between his family and his relationship with Megan and he confides in Kay; his wife tries to reconcile with him. Russert wrestles with the media demands about the case. Something from Bayliss' past comes out when they try to get the liquor license for their bar. Bayliss goes to the liquor commissioner to work things out. A collector of the macabre comes in search of the victim's white gloves. A third victim is discovered.
The church asks that the public know the details of the murders. Pembleton has an interesting time in the box with a witness who has multiple personalities and is shown to be the killer, but before he can get a confession, her lawyer arrives and later she confesses on television. Pembleton begins to question his faith. Bayliss becomes a not-so-silent partner. Beau spends some time with his family and decides to end his relationship with Megan.
A young man comes into the squad room and after getting their attention, tells the detectives that his brother has been shot. Pembleton is sued by the multiple personality serial killer, who states he violated her civil rights during interrogation; he is discouraged when the city agrees to settle out of court. Munch must attend an alcohol awareness seminar to meet a requirement for the bar. Lewis has "love at first sight" with a woman who makes models of crime scenes, but she has "love at first sight" when she sees Bayliss and he sees her. Later, they attend an art exhibition and have an unusual sexual encounter in her "bed." All is not well at the Felton household, when he returns home to a cleaned out house.
Bayliss continues his relationship with the artist, but she's told her boyfriend. When she tells Bayliss that her boyfriend hit her upon hearing the news, it makes Bayliss so mad he confronts him. Pembleton and Bayliss investigate the death of a woman who's received a delivery of fresh flowers, although she's been dead over two weeks. Bolander and Munch investigate the shooting of Thorne's source, who's linked to a cocaine cartel, then Thorne is shot. Gee tries to get the department to get him a replacement for Crosetti. Thorne's daughter decides to keep his newspaper going. Beau tries to find out where his wife has moved the family. With Meldrick and Bayliss' disagreement over the artist, Munch is left without partners for the bar. Bayliss goes over the edge when the artist dumps him, so he holds up a liquor store for 11 cents; Pembleton gets him out of it.
Crosetti's body is found and Bolander is the primary and he thinks the evidence points to suicide. If it is a suicide, there will be no honor guard for the funeral. Refusing to accept the death as a suicide, Meldrick launches his own investigation and tries to thwart Bolander's investigation. Bayliss and Pembleton make arrangements for the funeral reception. Pembleton has reservations about going into the church for the services. Munch works with his brother, an undertaker, to arrange for a coffin. The preliminary ME report shows Crosetti had a blood alcohol level of .25 and wide variety of anti-depressants, The verdict: suicide.
After uncovering the fact that an elderly woman's tongue was cut out, Kay decides it is time to take a vacation. She returns home and while she is there she looks into the murder of an environmentalist. The suspects include her brother, an ex-beau and their co-worker. Pembleton reluctantly becomes Felton's partner and they finish investigating the murder of the elderly woman. Munch is against having a television put in their bar.
Munch spreads his usual Christmas cheer. Russert, who misses detective work, joins Meldrick on an investigation into the murder of a material witness, when she discovers she knows something about the victim's case. Munch and Bolander investigate the death of a man in a Santa Claus suit and Munch spends the evening with whom they believe is the victim's son. Beau buys Christmas presents for the kids, although he still doesn't know where Beth and the kids are. Bayliss searches the station in search of a game of hearts.
Pembleton and Bayliss investigate the shooting of a young boy. During the investigation, the mother of the victim meets the mother of the shooter in the aquarium. The shooter shows no remorse for the killing, although he shot the wrong kid. Munch, Bayliss and Lewis can't remodel the bar when they discover it's been classified a historical landmark. Then when they find out back taxes are due on the building, which shuts them down before they open. Beau finds out his kids are in Upper Darby, Pennsylvania, so he goes to find them.
The deputy commissioner invites Pembleton to lunch and gets him to investigate a case involving a congressman. Beau hires a private detective to find Beth and the kids when his clue that they are in Wilmington falls through. Howard and Felton investigate a case of a dead homeless man. Their job is made more difficult when they can't find the body. Lewis and Munch investigate the death of a motorcycle gang member. Pembleton finds out the truth, participates in the cover-up and then resigns when the media gets hold of the real story and the deputy commissioner doesn't back him up.
Russert's old partner joins the homicide unit, but she suspects that he is taking his work frustrations out on his wife. Pembleton struggles with his pride and domestic life as Gee and Bayliss try to convince him to return. Bayliss is partnered with Lewis and on the way to the crime scene gets the ride of his life. Bayliss tangles with a reporter. Beau is in Philadelphia with his kids. The bar has its grand opening.
Bolander, Munch, Howard and Felton all meet to serve a warrant, but Bolander, Howard and Felton are shot in an ambush. Pembleton becomes the primary in the investigation and is partnered with a detective who specializes in the psychology of their prime suspect: a pedophile. Stan's ex-partner Mitch Drummond offers his help. Kay's father and Beau's wife and the kids come to the hospital. A clerical error is discovered to be the cause of why the detectives went to the door marked 201, instead of 210.
The detectives continue chasing their only lead, the child molester. Munch is teamed with Stan's old partner. Beau has no feeling in his foot, but feels guilt about Kay's condition. Stan's ex-wife arrives in town, but has a hard time going to see him at the hospital. Barnfather and Granger want Russert to review Gee and see if he was negligent in his duties regarding the paperwork that led to the shooting. The pedophile is located and it is discovered he was responsible for the strangulation of a young boy, but not the shooting of the three detectives.
Bolander has a relapse. The detectives sound off to the local news about the shooting. Apartment 201 is opened up and the occupant, Gordon Pratt, is a gun freak who once tried to be a cop. Russert and Howard declare a truce. They find the shooter, but lack of a weapon gets him released; later he is found with a bullet in his head.
Pembleton receives an extradited prisoner from New York City Detective Logan. Bayliss is put in charge of investigating the death of Gordon Pratt, but gets no cooperation from anyone on the force. Beau wants to return to active duty. A woman recognizes Munch from an old picture that is hanging in an art gallery across from the precinct. To Munch's embarassment he discovers that an old girlfriend, who's a photographer, is displaying an old picture of him in the buff at her gallery showing. Pembleton and Meldrick investigate a random shooting of a woman, and they clash over where the weapon may have been fired. They also find a woman who's shot her boyfriend and stuffed him in the freezer. Beau accompanies Gee on an investigation and must come to grips with his inability to look at a dead body the same way.
Beau meets Megan's cousin, NBC's Tim Russert. Kay and Stan return to duty, after Stan undergoes a final test, and Kay finds her desk has been moved. They like Beau, they both must get used to the job again. Tim and Beau investigate the discovery of a skeleton found buried in a backyard. Bolander and Munch discover an unlikely suspect in the murder of a quiet elderly couple: their grandson. Gee exposes Granger, who used his relatives in some department plumbing contracts; the information is leaked to the papers, Granger is forced to retire. Barnfather is made colonel and a new captain is named, Megan Russert. The higher ranks of the Baltimore police department are now more politically correct, but Gee doesn't like it.
A 16-year-old murder case must be reopened when the daughter of the convicted killer holds Col. Barnfather hostage. Pembleton and Bayliss investigate an elderly man whose wife died of drowning in the bathtub. Gee and the newly appointed Capt. Russert clash over the handling of the hostage situation. Bolander, Munch, Howard and Felton must go to the archives to find the records of the case. Lewis meets a strange homeless man who's witnessed the suicide of a man who committed the original murder and the detectives race to overturn the previous conviction. A new "old" bartender tries to convince Munch to go with the latest rage, microbreweries. Bolander and Lewis try to connect the suicide victim to the man on death row.
Crosetti's caseload is distributed among the detectives and Howard's 100% clearance rate may be in jeopardy when she gets his most difficult unsolved case; this is further complicated when Beau misplaces some new evidence. Gee meets one of Megan's friends at lunch and is convinced she isn't interested in him because he is too black. The guys close on the bar but wind up penniless when they must pay extra fees that they weren't aware of. Beau looks to Megan for comfort when he can't recover the evidence and it looks as though Beth and kids are never coming back.
Tim's cousin shoots a Turkish exchange student and his partnership with Pembleton may be in jeopardy when they both stand on opposite sides of the case. Lewis hires his grandmother to cook at the bar.
A convict is released from prison and begins to get his revenge on Frank by frustrating the investigation he is currently working on and also by terrorizing his wife.
Bolander and Felton are suspended for 22 weeks without pay for incidents related to activities at a police convention in Washington, DC. Howard plans to take the sergeant's exam. Pembleton and Bayliss are assigned to investigate the death of a body found at an arson. At the scene they meet an arson detective that clashes with Frank's working style. Frank hesitates chasing a suspect, and later we learn that his wife is pregnant. Munch also decides to take the exam, and when the wagering begins on who is going to pass, everyone favors Howard. While the detectives are debating whether the fire was set to cover the murder, another fire is started.
The fire investigation continues. Bayliss' back is acting up and Kellerman is paired with Pembleton. Kellerman shows Gee something, so he is offered a transfer into the department that he first rejects. Kay takes the sergeant's exam, Munch misses it due a "comedy of errors."
A gas leak causes the detectives to evacuate the building, so they relocate to an old bank building. Lewis is paired up with Kellerman on the murder of a woman. Sergeant Howard tries to carve out a place for herself with the other detectives, but her efforts prove unpopular. Pembleton has trouble adjusting to the new surroundings and his wife's pregnancy. A cameraman who was at the scene of the murder has who he thinks is the perpetrator on tape; however, when he brings the tape to Gee, he is thrown out before he can say why he's there. The cameraman eventually strikes a deal with Lewis and Kellerman.
The squad returns to the station. The FBI joins with the detectives to stop a "thrill killer" who's working his way north on I-95. Gee tries to reconcile with his daughter. The killer smells a rat at a roadblock so he bails out of his pickup. Everyone mobilizes to find him and when they do, the suspect in custody, while identical to the killer, claims he is innocent.
Pembleton and Bayliss investigate a murder that was committed in a gay neighborhood by skinheads and the victim's sexual preference is questioned. Brodie is hired by the department to videotape the detectives' crime scenes. A voice stress analyzer is brought in for a demonstration. Meldrick gets a lead and closes an old Crosetti case that even Howard couldn't crack; it causes a little tension between them.
Technically it's not a homicide; however, Pembleton and Bayliss investigate the "murder" of a small boy who's the victim of a stray bullet, which makes him brain dead. The parents must choose what to do with their son. The Pope is in town.
Lewis and Kellerman interview a suspect and uncover a 10-year-old crime, which is assigned to Howard and Munch. Tim lets Frank's secret about Mary's pregnancy slip out. Howard and Munch find the body from the 10-year-old murder bricked up in a wall. John has a date with Alyssa, the ME, but finds himself in bed with her new roommate before their date, so he begins avoiding her. Howard and Munch's murder suspect has a fascination for former Baltimore resident Edgar Allan Poe. Munch plays up that angle while trying to break their suspect.
Jay Leno stops by the Waterfront Bar while in town visiting his cousin Mary; Munch and Bayliss don't want to bother him. A new year starts out with a clean board and Brodie begins his work taping with the detectives. A sniper takes the city hostage, threatening to and executing people every 8 hours. The sniper uses Hangman as a way to leave clues for the detectives. Bayliss is the primary and his back is giving him trouble as he worries about surgery his doctor wants him to have. To combat the pain, he keeps taking muscle relaxants. A suspect is found and cornered and he shoots himself before they can take him into custody. Russert gets demoted when Barnfather doesn't like the way she handled the investigation.
The sniper continues the shootings and everyone returns to duty lacking sleep. The media starts to make their presence felt. Munch begins to worry about Howard's safety, fearing she'll be wounded again. Frank makes his wife wear a bulletproof vest. Gee asks for Russert's help even though Barnfather had ordered her to stand down during the rest of this investigation. A man at the scene of both of the day's shootings is put into the box for questioning. Russert has a talk with the suspect with the subject being keeping people's attention and respect.
Gee is sent upstairs to see Barnfather and everyone speculates about the vacant Captain's position. Lewis and Kellerman are sent to Pennsylvania to extradite a woman back to Baltimore where she is a suspect in the murder of her husband. Munch tries to find a videotape in Brodie's pile. Later after reviewing the tape, they discover a key piece of evidence isn't contained on the tape. Munch wants the tape erased, but Brodie delivers the tape to court and that results in the outcome Munch feared. On the trip back from Harrisburg, Kellerman convinces Lewis that they have time to stop at Neptune's Castle and they lose the suspect, for a moment. Later they lose her again but find her at the house of her dead husband's mistress, delivering a hat. Much to everyone's surprise but not the viewers Gaffney is promoted to Captain over Gee. Captain Gaffney lays down the law.
Lewis and Kellerman try to subdue a large man who's gone on a rampage. The large man is finally subdued and they find him digging up his mother. This case brings out some information about Meldrick's family, and he tries to see his brother, who doesn't want to see him. Kay tries to keep the identity of her new boyfriend a secret, mainly from John, which drives him crazy. Pembleton and Bayliss investigate the death of a man whose body is found in a car. Scheiner says he died from internal bleeding, not the gunshot wound to the groin he was treated for at an emergency room earlier that day. They discover that the doctor may have had a motive for doing a less than adequate job treating her patient.
Continuing the investigation in New York City, Egan's wife is questioned by Frank and Tim. Just a few hours later, Egan's wife is killed and Egan's son is seen running. Kendall is taken into proctective custody until he gives up the suspect's name. Lennie Briscoe and Rey Curtis (From Law and Order) come to Baltimore. Munch finds out that Lennie knew his ex-wife a little too much (She moved to NYC after divorcing him). The suspect tried to escape in a seaplane but is caught. NYC ADA Claire Kincaid comes down to extradite him back to NYC, which made Frank upset. While extraditing him, the suspect has a heart attack and dies at the train station.
Russert and Munch are assigned to work a case together; they find a retired cop who was murdered near his wife's tombstone. The dead cop's son asks Lewis, whom he went to the academy with, to get involved with case. He also makes his own inquiries, which get him into a bit of trouble. A suspect is arrested; however, despite the overwhelming evidence against the accused, the jury acquits him. The son contemplates delivering his own justice.
Jake Rodzinski has trouble dealing with the verdict of the trial and takes justice into his own hands. Kellerman is back from a family wedding in Wisconsin picks up the case of the murder of Kenny Damon. Lewis is not allowed to know all the details of Kellerman's investigation, because of his past relationship with Rodzinski, their chief suspect. Bayliss is at odds with Pembleton over the disposition of a grilled cheese sandwich.
The entire squad is put on 24-hour surveillance when a mass murderer has been identified, isn't at home and doesn't know that they know. Gee debates leaving the squad in the midst of the stakeout, so he can attend his daughter's wedding in California. As the detectives rotate through shifts on the stakeout, the main topics of discussion are the homeowners and Bayliss' plans to leave the unit.
A young girl is murdered, in a style similar to Adena Watson's murder. Frank demands to work the case alone as Bayliss begins to think that the two crimes might be related. Bayliss' obsession with trying to get this case solved and linked to Adena's murder causes the two of them to clash. Howard learns that Brodie has a crush on her and tells him she doesn't like the joke that's being pulled-- only problem there is that it's the truth.
Kellerman and Lewis (with Brodie) investigate a shooting at the New Moon motel, where everyone there has a motive for the crime. They split up and canvass the denizens of the motel; Lewis also searches for the victim's missing boot. The murder is just one of the many crimes that has occurred or is occurring at this establishment.
Lewis and Kellerman's investigation of a murder in a housing project puts them at odds with a civilian-patrol group, run by the Black Muslims. Munch is excited because Stan is scheduled to come back June 1st. Russert and Munch catch a case where both the victim and shooter are dead. She with Howard must decide whether to circumvent the so-called "blue wall of silence" among police officers when it is discovered that the officer on the scene didn't react in time. Barnfather stops Lewis and Kellerman's charging of a Muslim, until something is leaked to the newspapers. The "big man" is scheduled to come to the bar, but changes his mind, twice.
A prominent attorney is murdered and the murderer presents himself to Pembleton and Bayliss with a videotape that implicates him. Brodie works on increasing his self-image. Kellerman is determined to find out who's the "lunch bandit." The NSA steps in on Pembleton's murder investigation and provides him with a guilty party, even though they know he didn't do it. Bayliss' disgust with the interference doesn't sit well with Gaffney who wants to charge him with insubordination.
Lewis and Kellerman investigate a series of homicides that put them into the middle of a drug war. Kellerman suspects that Lewis is seeing someone, but he doesn't "kiss and tell." As the red piles up on the board Gee gets edgy. Kellerman seeks comfort from the godmother of the daughter of the victim's family. Kellerman and "Drak" have a confrontation. At a "Peace on our Street" demonstration, the current drug war is ended.
A trash-talking radio talk-show host makes a proposal to his listening audience. Lewis announces to Kellerman that he is getting married today, then he throws up. He motivates the rest of the squad to help him with the final details as he is getting married "tonight after the shift ends." Kay brings her sister with her to the station. Since the whole squad is busy with Lewis' wedding, Gee takes Howard out to work the homicide of the radio talk-show host. One of his listeners took him up on his proposal. Munch is skeptical about the Lewis wedding; he thinks it's an elaborate practical joke. Bayliss and Kellerman vie for the attention of Kay's sister. Gee shoots and kills a potential suspect, but the suspect was in jail at the time of the talk show host's murder. The guy who fingered him admits that he did it as a joke. The wedding is no hoax. During the festivities Pembleton's wife goes into labor.
Mary gave birth to a girl named Olivia; Tim is more excited about it than Frank. Their latest case involves a multiple shooting a restaurant. Lewis is back from his honeymoon, but while working a case with Kellerman, he confesses that they have yet to consummate their marriage. Later he tells him that they've separated. Tim stops by to see Frank and Mary's baby. They get a suspect for their case in the box. Frank collapses in the box while interrogating a suspect. Frank is put under the knife to release the pressure built up in his head from the stroke he had. After the surgery the doctor tells them that he doesn't know if Frank will recover.
Gaffney and Barnfather give Gee a hassle about the return of Frank to duty and the sudden departure of Russert to Europe. Bayliss and Munch are called to the scene of a homicide, where the victim, Mrs. Uba, was cooking breakfast and the only witness may be a male pig named Angie. Frank returns to work and Gee tells him what his limited duties are going to be and that he's called in all his favors and both their asses are on the line. The squad is called out for a hostage situation at a middle school.
Night has fallen and the crisis is no closer to being resolved. Gee demands that Barnfather make a decision. Frank continues to trying to adjust. Frank insists on going to the hostage scene. The identity of the hostage-taker is made when he demands that his pig be brought to the school. When the pig doesn't arrive in time, he sets a fire and seriously wounds a hostage (who later dies) and then becomes badly burned. Brodie takes issue with Munch's treatment of Pembleton. The paperwork gets completed and the hostage-taker is formally charged. Frank makes a decision regarding his recovery.
A riot breaks out at the prison, where two inmates are killed. The squad goes to the scene, but Frank must still stay behind. Bayliss, Lewis, Kellerman and Howard interview the inmates; many of them have familiar faces. Frank works on his target practice. Bayliss thinks that one inmate really wanted to tell him something, so he puts together a deal to get the information. The inmate confesses to the murder and Bayliss doesn't believe him. Another riot breaks out and the truth is finally discovered.
More drug-related homicides are occurring. Pembleton is still relegated to desk duty and now so is Kellerman. A federal grand jury investigation is being conducted that goes back to the time when Mike was in the arson unit. Frank is still not taking his medicine and getting ready for the range test. Brodie moves out of Munch's place and into Bayliss'. Lewis finds out that the witness to his drug homicide has been brought downtown. He goes after him and meets Stivers, a female detective in narcotics. Lewis's witness points toward Luther Mahoney as the initiator of the contract. They go to find the executor, who's been executed. Stivers pages Mahoney and he comes in for questioning, but they can't make a case that Danvers thinks will stick. Frank misses a passing grade on his test by four points.
The new Chief Medical Examiner (CME), Julianna Cox, speeds into town. An FBI agent, Pandolfi, conducts interviews with the squad about Kellerman. Frank looks for way to celebrate his anniversary with his wife. The new CME arrives on the scene of a homicide that Lewis and Bayliss are working on, they lay down their respective ground rules. Bayliss' murderer confesses to committing another crime. Kellerman is worried by the ongoing investigation and takes it out on another arson officer. Brodie offers to make chili for the Lewis family but the dinner turns into a fight for Meldrick and his wife. From a suggestion by Frank, Bayliss and Lewis get the other body exhumed and checked out. Frank and Mary celebrate their anniversary. Bayliss gains some insight into the new CME.
An article appears in The Baltimore Sun about Kellerman and the other members of the arson unit who are under investigation. Munch investigates the death of women whose husband returned home to find her dead, cause unknown. He suspects the husband but Cox thinks differently. Pembleton tries to help Bayliss close the Lambert case. The article puts Kellerman on edge and he goes to Roland's office where he discovers Roland is a federal witness. This incident gets him suspended until he takes a polygraph test. Brodie gets an offer to stay at Kay's place. Munch presses his witness and breaks him but Cox's evidence still says otherwise. Kellerman takes the test and while waiting for the result tells Lewis the truth. Cox visits Munch's suspect in his cell. Frank reflects on his past and the future. Kellerman passes the polygraph, but so did the federal witness; one of them beat the test.
Family members of murder victims (Widmer, Rath and Silvio) are in a support group where they discuss their feelings about the loss they have each suffered. Short-handed, Gee investigates the Widmer homicide at the Waterfront Bar. Bayliss' homicide is unidentified for 48 hours before she is identified as being Rath. Lewis and Munch investigate a car jacking at Federal Hill, where the mother is the victim and the 3-year-old daughter in the car at the time is missing. Meanwhile, Howard, Kellerman and Pembleton stay behind. Frank interviews the two witnesses that Tim had in for questioning and gets a lead on a suspect. Cox joins the support group meeting late; she is still coping with the death of her father.
Lewis and Bayliss investigate a homicide at a boarding school. Gee goes to Frank's house to pick him up for a trip to the gun range. Kellerman wants the investigation into corruption in his old arson unit to move along, but he finds out that all the real guilty parties have made plea bargains. Frank's firearm test looked promising. The tiny little voice in Bayliss' head tells him that McPhee Broadman might be their suspect despite the fact that his mother is a powerful judge in Baltimore. A student comes forward and confesses to the student's killing; however, the detectives aren't convinced he alone was responsible. Frank passes the exam and can return to active duty, but as far as he is concerned the real test is in the box.
Pembleton waits with anticipation for the phone to ring. It does and with Bayliss as the primary, they proceed to investigate the triple murder of a divorced woman and her children. Kellerman asks Brodie not to return to the boat. Lewis and Munch get a homicide that they can track back to Luther Mahoney. Bayliss and Pembleton disagree on who the primary suspect is in the murder. Mahoney's nephew wants to remain "monogamous" in implicating his uncle. Kellerman gets his summons to appear before the grand jury. Frank and Tim must work out the finer points of working in the box together again. Mahoney's hand reaches out from jail and silences his nephew; the case is a bust. Lewis lays down the law to Luther Mahoney in the Waterfront Bar. Cox finds Kellerman and his predicament intriguing and offers him some company, the night of his summons.
Frank gets his first case as a primary-- unfortunately it is a case that involves the shooting of Danver's fiancée. Danvers is concerned about Frank being the primary and keeps throwing his opinions into the investigation. Danvers changes his perspective on the death penalty and also reflects on his past performance in many of the cases he's tried. Brodie continues to look for housing; the latest place he tried staying was the morgue. Kellerman is discouraged when it appears as though Cox may have only been looking for a one-night stand and nothing more-- so he takes a sick day. Gee takes some time out of his day to have a talk with Kellerman's former partners to see where they stand with him in regard to their testimonies to the grand jury. He also sees the Deputy Commissioner to see what can be done for Kellerman; what he learns instead are some truths about the Gaffney promotion.
On New Year's Eve, the detectives sit back in the quiet of the evening and watch a documentary that Brodie has made about them and their work. In this documentary, entitled "BACK PAGE NEWS: Life and Homicide On The Mean Streets Of Baltimore", one of Frank and Tim's cases is covered where some "lies and hidden truths" are revealed. During a sequence about one of Mike and Meldrick's cases, they chase a suspect right into the filming of something called "Homicide" by director Barry Levinson and his crew. Mike and Julianna agree to try a date. Also, the identity of the "lunch bandit" is revealed to be Gaffney. Brodie reveals that the documentary has been sent to PBS and gives his reasons why. As the new year rolls in, things return to normal as the phones start ringing.
Frank and Tim investigate the death of a young girl whose abused body was found by the side of the interstate. Brodie goes to an interview with a new potential roommate. Kellerman finally gets his day in court, where he is supposed to take the 5th amendment. Frank and Tim disagree with their pursuit of the investigation. Frank tries a different approach with the mother and she tells him the story-- only they won't be able to get a murder one conviction. Julianna comes down to the courthouse to offer Mike some moral support. He sees Connelly come out of the courtroom and thinks things are going bad, so he prepares to give it all up. However, his appearance before the grand jury doesn't go quite as he expected. Brodie walks out of the building with his new roommate. The detectives try to celebrate Kellerman's freedom, though he has different thoughts about the situation. Tim tries to come to grips with the child abuse he experienced in his past and also tells Frank he doesn't want to be partners anymore.
Kellerman is disappointed with his treatment in the press (or rather the lack of it). Back on the job, Mike gets his first case. There was a shopkeeper who was killed for chasing the drug dealers out of his corner. The prime suspect is Luther Mahoney. Frank tries to reconnect with Tim who is still resolved to no longer be Frank's partner. Mike is visibly on the edge, with all the pressures of the past months and his reputation tarnished, and agitated by the fact that Luther Mahoney may get away with another murder. Meldrick tries to talk him down, not anxious to lose another partner.
Kellerman assures Lewis that he is seeking some professional advice; he also takes some time off. Lewis is assigned to work with Pembleton and neither is happy with the situation. Together they investigate the murder of a wealthy woman. They suspect the brother may have had a touch of sibling rivalry. Meanwhile, the brother insists that the police have stolen his sister's diamond ring. Mary tells Frank that she thinks they need to talk to a marriage counselor. Cox investigates whether the missing diamond ring might have been taken by one of her staff. She gets Brodie to help her add some video surveillance to the morgue. Mary asks Tim to be Frank's partner again.
A new Baltimore Sun reporter gets into the middle of Frank's investigation of the death of a county cop who was shot because of drugs. Gee likes her style. Mike's brothers, Drew and Greg, come to town, who want to take him and his boat to Miami to set up a charter service. Mike learns that they are on the run from a bookie that Drew owes $18,000. To pay that debt, they've stolen Babe Ruth's Baltimore uniform from another bookie with the intent of selling it. Lewis and Cox go in search of the Kellerman boys. They find them in jail where they spent the night after trying to return the uniform.
Brodie suggests that a classmate of his named Schack should be a suspect in the death of the student that Munch believes committed suicide. Frank and Mary meet with their marriage counselor and they begin to air some issues. Bayliss and Kellerman try to link together two deadly bombings. Schack attacks Brodie, but he can't prove it. He does offer a way to get Schack to admit to the murder. Frank tells Mary that he will agree to getting Olivia baptized. Mike connects the two bombings; the victims were both connected through the death of the Korean grocer who was murdered by a man who worked for Luther Mahoney. They suspect that there may be more bombs, including one at the courthouse where Meldrick and Julianna are waiting to meet with Judge Aandahl and Danvers, both of who were associated with the Korean grocer case. Frank arrives late to the baptism; Mary takes this as a sign and tells him she is leaving him for a while.
A woman that Munch had a crush on in high school is found murdered. He struggles with his faith as he works with Kellerman on the case. Meanwhile, Frank also struggles with his faith and the fact that Mary has left him.
A girl complains to the desk sergeant about her father's abuse of her mother. Meldrick spends the night remembering Crosetti with the Chris and Eva Thormann. Chris reflects on his own memories of the shooting incident that blinded him, the shooter is now up for parole. Bayliss with Pembleton investigate the homicide of a man shot to death in his own house. The shooter, the murdered man's wife will testify, is their daughter. The case triggers a painful memory for Tim who goes to visit his Uncle George.
A man transporting 72 condoms filled with heroin bound for Luther Mahoney is found dead in hotel. The department takes this opportunity to set up "Operation Get Luther." The operation almost goes off as planned, except Luther Mahoney gets Lewis' gun and is holding it on him as Kellerman and Stivers enter. Frank and Tim agree to become partners again. Tim stops by to see his uncle. Munch takes a call from a convict who was looking to talk to Bolander. He has information on an old murder case that should be a done deal. That involves the digging up of section C of the parking lot at a racetrack. Munch discovers that the supposed victim is alive; however, he isn't that way for long.
There is a major police chase after an armed suspect, as he holes himself up in a row house that is the headquarters of ARM (African Revival Movement). The head of that house, a former cop, calls in a favor, high in the police department. Munch and Pembleton try to work the case as Bayliss seems to be missing. Their investigation seems to be thwarted every step of the way. Stivers' has second thoughts about what she saw at the Mahoney shooting. An attempt to serve "Burundi" Robinson an arrest warrant breaks out into a war between the police and ARM. Gee goes into the house to confront Robinson and finds out who and what he knows.
Bayliss has disappeared again as Pembleton and Brodie make their way to the scene of a shotgun suicide. The victim appears to be Beau Felton. Gee's letter, including information gained in the "Burundi" case, begins to make an impact at the highest levels of the department. Frank returns to the department with the news about his case. Lewis goes off, wondering who is going to be next. Det. Falsone comes to the squad with news about why he thinks Beau Felton killed himself. Lewis and Stivers discuss the Mahoney shooting. Cox finds something interesting about the Felton case; she digs in deeper and the results change the case to a murder. Bayliss turns up the next day and disappears again to his Uncle George's place. Pembleton and Howard try to work with Falsone to find Beau's killer. Gee finds out that Beau had been working undercover for the past six months on the Cantwell auto-theft ring. Megan Russert returns from France.
Mike and Julianna wake up the morning after a night of drinking and passion. The investigation into Beau's death continues; Howard wants to be the primary while Frank tries to maintain control. Gee asks her to step aside and let him do the job with a more unbiased approach. The investigation creates some unlikely pairings: Pembleton with Gharty and Bayliss with Falsone and Munch on his own. Meanwhile, Howard and Russert make arrangements for Beau's funeral. Lewis and Kellerman's investigation into a homicide is stalled; when Kellerman's hangover laden police work is shoddy. When it appears as thought the investigation is going nowhere; Kay demands to be put on the case. Gee refuses. Because of his bad day and finding Julianna drinking with someone at the Waterfront Bar, Kellerman suggests that they should stop drinking. Frank tries to call Mary; eventually they connect and reconcile; with Frank saying that he is willing to give it all up. They find out who killed Beau, but when they go to arrest him, they find he is gone. Government officials offer commendations for Beau and Gee eulogizes him. Gee also finds out there will changes in the department next year; members of the squad may be rotated into different departments in 3-month intervals.
Their rotation in robbery is up, Frank and Tim return to the homicide unit. They find that citations are being handed out to the unit and a delighted Gee, whose clearance rate is the highest it has been in five years. Kellerman and Lewis are also scheduled to return. Howard is still on assignment with the fugitive squad. Additions to the unit through rotated assignment include Det. Ballard who actually comes from a Seattle homicide unit, Det. Falsone and Det. Gharty. Falsone and Gharty worked with the unit on the Felton case last spring; however, nothing is mentioned about the status of that case. (Sharp-eyed viewers note that Felton's name is still in red under Pembleton's name on the board.) Meanwhile, Gee attends a black tie function honoring Felix Wilson, a respected member of the community. Because he grew up with them, Gee sits at a table with Felix, his wife and their family. Everyone attending the function at the hotel is kept late because the body of a woman is found dead in the men's room. Pembleton is the primary and the victim is identified as being a housekeeper in the employment of Felix Wilson. Pembleton's handling of the hotel murder frustrates Ballard. She doesn't think he is moving in the right direction, questioning the Wilson family. While they are out driving, someone using fifty caliber bullets shoots at Lewis and Falsone. In addition, Stivers is interviewing a woman who is also shot with a fifty-caliber bullet, coincidence? Kellerman is mad at Lewis because Lewis indicated he didn't want to be partners again. The pieces come together after a fifty-caliber bullet wounds Kellerman in the arm. No longer a coincidence, the key that links these three cops is Luther Mahoney according to Falsone. Falsone wants to know what actually happened at Luther Mahoney's place; however, Lewis or Kellerman aren't talking. The department begins to apply pressure on Mahoney's former associates and discover it is actually a family thing. Luther's sister is taken into custody and she mentions that she has a surprise for Kellerman.
While Pembleton is still interested in the housekeeper's ex-boyfriend, Ballard still thinks that the Wilson family needs to be looked at more closely. Also, a body is found at Camden Yards during a game between the Orioles and the A's. Falsone questions Stivers about the Mahoney shooting and that begins to make her nervous. Tensions mount because there appears to be a leak to the press within the unit about the Wilson case. Orioles' security wants the case quickly resolved. Munch and Kellerman have only 48,000 possible suspects. The victim is discovered to be a dead Yankees fan. Tim gets his old high school French teacher to help them check out the whereabouts of the housekeeper's ex-boyfriend. He is cleared because of his current incarceration in a Haitian prison, which leaves the Wilson men as more probable suspects. Are Gee and Pembleton protecting Felix Wilson because he is a prominent businessman in predominately black Baltimore, as outsider Ballard suggests? Munch and Kellerman get lucky in their search for a suspect, but the man they find wants to see the end of the game before he will talk. Falsone keeps digging into the details of the Mahoney shooting. Frank gives in to pressure and brings Felix Wilson into the box where he gets a confession. Felix Wilson confesses to having had sex with his housekeeper, but nothing more; he also agrees to provide a blood sample. However, his attorneys arrive later with an order that will keep the Wilson family from further questioning and any testing.
The Wilsons go on television to offer a reward. The newspapers are making the Homicide unit look bad and Barnfather wants quick resolution to the case. The man (and his wife) who gave up Junior Bunk are murdered; Falsone and Lewis investigate. The only survivor, their young son, is brought in to find out what he remembers. His memories-- and a recorded phone message-- lead Stivers to believe a former member of the Narcotics unit is involved. The officer cops to a deal that implicates Georgia Rae Mahoney, though Giardella doesn't want to pursue that yet. Falsone's questioning of the Mahoney shooting leads Cox to doubt her actions at the time of the investigation. Incriminating evidence leads the detectives to Hal Wilson being their prime suspect. Frank goes to interview Felix and Hal Wilson; son and father confront some long-standing issues. Hal's confession is inadmissible in court, the Wilsons leave the Baltimore area, and the case remains officially open.
A young woman is viciously attacked. Falsone and Lewis are called to the scene because the victim wasn't expected to make it. Stivers is working in Sex Crimes and is second to the scene; however, because Homicide was first it is technically their case. The attack is the third in three months and the bosses decide they'll work the case together. Frank's wife is overdue on her delivery. Tim recommends a restaurant whose salad has been known to "kick start" delivery in pregnant women. Frank gives it a try. Georgia Rae Mahoney meets Kellerman and mentions to him that she has a surveillance tape from Luther's condo. She tells him she'll keep in touch. Kellerman tracks down the old surveillance equipment from Luther's condo. A possible suspect is found in the rape case that doesn't turn into anything. A recanvas of the bars brings a new suspect to light. The salad might have worked its magic, because Mary gives birth, although there are complications that cause Frank to think about the job's effect on his family obligations. Kellerman meets Georgia Rae Mahoney at Luther's grave; she is not sure what she wants from him, yet. The victim dies from her injuries.
The young man that was stalking Brittany in Baltimore is interviewed and relates that he saw her being attacked by someone. When going to question the parents, the New York and Baltimore detectives discover that the Janaways have returned to Baltimore, so they make the trip to Charm City. They get the father in the box and he demands that they prove he did it. The attorneys fight over jurisdiction, but the judge rules in favor of Baltimore and the two teams of prosecutors must work together. When the father is put on the stand he gives an alibi, a surprise that gives the detectives 48 hours to verify this alibi. When the alibi checks out, they bring in both of the parents to get to the truth.
Two Vietnamese teenagers witness the shooting of their parents and some friends. One of the friends was a cop and one of the shooters they say was another cop. That cop they discover failed her psyche evaluation but may have possibly gotten her job due to Affirmative Action; although strings pulled by her father proved to be her ticket into law enforcement. After they are able to implicate the cop in the shooting, as a bonus they discover the body of her string-pulling father. Ballard suffers from an allergic reaction to crabs. Falsone finds out that the case against Georgia Rae Mahoney is going to be dropped because of a lack of evidence. He suspects that the whole Mahoney thing is going to blow up in the department's face, because he knows the Mahoney shooting didn't go down the way Stivers, Kellerman and Lewis reported it. Kellerman debates with Cox about what he should do about the Mahoney situation.
A man falls between the cars of a subway train in front of horrified witnesses. Was he pushed? While the man is still alive, the prognosis is he will be dead the moment they extract from the position he currently occupies: pinned between the train and platform. Homicide is called in light of this condition and the fact he may have been pushed. Pembleton questions the victim, and Bayliss questions the witnesses, especially a strange one named Larry Biedron. The victim has no relatives in the Baltimore area. He does have a girlfriend who is supposed to be jogging in the area; Lewis and Falsone try to find her to bring her to the scene.
Ballard and Gharty investigate the death of a man at a laundromat. The Waterfront Bar gets ready for the Christmas holiday. Munch's ex-wife, Gwen, shows up; her mother (a literary critic and author) has died. Tim goes Christmas shopping and runs into Julianna; he invites her to come to the Waterfront's Christmas celebration. Ballard and Gharty interview the victim's girlfriend (as listed in his address book). Cox informs Ballard and Gharty that the victim was HIV positive and she also convinces Kellerman to tell Lewis and Stivers about the Mahoney videotape. Munch gets his brother to give Gwen a deal on her mother's funeral arrangements. The victim's mother knew about his HIV status and about a girlfriend he didn't use protection with, whose name didn't appear in the address book. Ballard and Gharty find this woman and find that she has full-blown, terminal AIDS, and they bring her in for questioning. Ballard feels the woman has suffered enough so she is reluctant to a get her confession and file charges. The funeral service is held but no one shows up except for a paid mourner and author Peter Maas, who just wanted to make sure she is dead. Kellerman tells Lewis about the videotape. Tim gives Julianna a present and kiss.
The semi-nude body of a man is found in a dumpster outside of a restaurant. Bayliss returns Cox a pair of her earrings that she'd left at his place the night before. Disturbed by him doing that in public and while at a crime scene, she suggests they take some time off, instead they decide to break it off. The owners of the restaurant thinks that this murder might be tied to another murder (one that Munch is working). Lewis confronts Kellerman about the Mahoney videotape and the need to let Stivers know that she is also "in the soup." Lewis tells Stivers about the videotape, so she demands a meeting with Kellerman. Falsone confronts his ex-wife about getting to see his son more often; however, they argue and he plans to pursue getting joint custody. Kellerman decides that he will try to force Georgia Rae's hand, since he doesn't plan on doing anything corrupt for her anyway. Kellerman tells Georgia Rae that she can do whatever she wants with the videotape, he doesn't care. Bayliss decides he is going to take Chris up on his dinner invitation. Georgia Rae sends Kellerman a videotape, wherein she tells him that there was no security videotape; she was testing him to discover if he did murder her brother. Now that she is convinced he did, she promises retribution.
A white man is found lynched in a historic black section of the city; Falsone and Lewis investigate. The day after Tim's dinner date with the male restaurant owner that Tim was positive about, Frank is perplexed by Tim's interest in Laura Ballard. The autopsy reveals that the hanged man was also whipped. Gharty worries about Ballard getting involved with "switch-hitter" Bayliss. Lewis is convinced the lynching is related back to the victim's Civil War ancestor, infamous runaway-slave catcher and free-blacks abductress. Tim and Laura attend an art show.
Julianna wins the recognition of her peers. At dinner, Julianna and her colleagues swap stories about how they've cracked cases. Julianna relates a story that happened a few weeks earlier, a suicide might actually be turn out to be murder, when it is determined that the victim was shot in mid-jump. A bickering elderly couple proves to be the key to the crime. Meanwhile, Falsone investigates the legal possibilities of obtaining custody of his son. Ballard and Gharty investigate the death of a drug dealer, which takes them up into the hills of western Maryland in search of their suspects. Georgia Rae Mahoney sues Stivers, Lewis, Kellerman, Giardello, Cox, the department and the city for the wrongful death of her brother, to the tune of $60 million. Lewis confronts Georgia Rae and winds up with a suspension for his trouble.
Kellerman is trying to find Lewis, who's disappeared since his suspension. Bayliss is on vacation. Stivers rotates into homicide and Kellerman isn't happy to see her. A priest is found murdered. Falsone attends a custody deposition hearing. A tape is delivered to Channel 11 that contains some startling information from a Swami about the priest's activities involving young boys. Munch and Kellerman seek out the two boys who were at the scene of the crime; meanwhile the other detectives seek out the Swami. Both are located, though the boys do not provide anything conclusive; they are held in protective custody. Kellerman searches for Lewis. Meanwhile, church members protest in front of the station house. Falsone gets his son for a weekend. Ballard and Gharty detain a corner kid who might be identifiable as one of three who had frightened a priest. Unfortunately, that priest (a monsignor) can't make a positive ID. Because of public pressure, the boys are released from custody to stay with Sister Attwood. They run away from her home and later the monsignor is found murdered.
With the addition of the latest murder, the "red ball" investigation continues full force. The detectives and the returning Bayliss pose as priests in an attempt to flush out any leads. Munch's cover attracts two young thugs, but they prove to be nothing. Gee is called upstairs, where his performance doesn't sit well with Barnfather. Lewis turns up and seeks some help from Falsone. Pembleton receives a call that the two missing boys have been found. Pembleton and Stivers travel to collect them. Meanwhile, Gharty and Ballard find the pawnbroker who had accepted a stolen chalice. Cox and Bayliss prevent a drunken Kellerman from driving home. Ballard and Gharty use the pawn-receipt false address to track down the corner kid with whom they'd previously had a run-in. They bring him into the box and Gharty loses his cool. The kid is tough to crack, but Pembleton has an idea involving the morgue and a trip to the shore. While stumbling home, a drunken Kellerman decides he doesn't like the look of someone, so he cuffs him and leaves him for the uniforms that arrive on the scene. Falsone provides Lewis with the info he wants. Kellerman spots Lewis, who takes off. Pembleton's ploy works as the corner kid gives up the perps.
A slightly intoxicated man (driving with his wife) aggressively whips his car around a state-owned truck; the offended truck driver rams their car; their aggression results in a collision where both drivers die. The man's wife is in serious condition. Kellerman and Munch investigate this case. Falsone gets prepared for the final hearing in his bid for custody of his son. Meanwhile, the other detectives investigate the death of a man who made a mobile phone call from the coffin in which he had been buried alive. The coffin was buried in the parade ground of an old spy school. The victim might have remained alive if the lid hadn't been sabotaged to collapse. In the car / truck collision case, Cox's boss wants her to "verify" the results of the car driver's blood alcohol level to help protect the state from serious litigation. An old Russian friend of Gee's furnishes them with information that leads the detectives to the discovery of a group of men who couldn't make it as spies. (They call themselves the Silent Sons.) Cox asks Gee for advice on leaking the truth to the press. Falsone loses his custody battle. Cox is asked to appear before the state director of Health when he doesn't show, the secretary passes on a message from him: Cox's services are no longer required. The nut running the Silent Sons comes into the squad room, wrapped in dynamite. Bayliss talks him into the box. Julianna hits the road, heading north on I-95.
Pembleton and Falsone look into the death of an elderly man who might have been killed by the pit bulls owned by his grandson. The other detectives hang out at the Waterfront and tell stories about stupid criminals they have met. The judge in the wrongful death suit of Luther Mahoney decides there is enough evidence to turn the suit into a jury trial. Kellerman suspects there might be something up, so he tries to go and see the judge.
Homicide is called in when a woman is distressed at the fact the Dr. Turner helped her brother stop suffering from his colon cancer by injecting him with a lethal dose of morphine. Other members of her family were comfortable with the way he died. Pembleton and Bayliss investigate the issue of murder or mercy. Ballard and Gharty spot their city goats at a shopping mall, where Gharty was using Ballard as a consultant in his purchase of a gift. Stivers and Falsone catch a case where a schoolgirl and the owner of a pizza parlor are murdered during the holdup of the pizza parlor. Kellerman confronts Judge Gibbons and tapes their conversation about his ruling in making the wrongful death suit a jury case. Ballard and Gharty round up their city goats after they confront their mother. Gee warns the rookie homicide detectives, Stivers and Falsone about the baggage that comes with working their first case involving the death of a child. Pembleton and Bayliss' investigation of Dr. Turner's practice reveals that at least one of her patients didn't have a family to speak for him. Kellerman plays a tape of his conversation with the judge for Lewis. Gharty gives a gift to Billie Lou, the Waterfront bartender. Bayliss goes "home" when Pembleton puts Dr. Turner in the box.
A four-year-old boy is abducted while riding a merry-go-round in the park under the supervision of his mother. The Homicide unit, which helps in the investigation of all child abductions, is called in and Falsone is the primary. When the boy's father has an alibi that checks out, the detectives beginning to check on known pedophiles and later they receive a call from the possible kidnapper. When that doesn't pan out, they start over. The host of a nationwide television program, This Weeks Wanted, suggests that they hypnotize the little girl who was riding on the horse next to the boy. Hypnosis reveals a partial plate number and that leads to a lucky break. Ballard and Stivers discuss motherhood and Falsone checks on his son.
Munch and Gharty probe the death of a high-school athlete who appeared to have everything going for him. Pembleton and Bayliss have only one lead to a potential suspect, a pager number; however, Bayliss has a plan that should lead to the apprehension of their suspect. Kellerman and Ballard get a case with a drug dealer that Kellerman is less than enthusiastic to work. The victim is one of Georgia Rae Mahoney's lieutenants and there are four other unsolved murders in the last two weeks where the victims were members of the Mahoney organization. Pembleton and Bayliss apprehend the wrong suspect, but the fact the suspect was trafficking 200 Kg of narcotics gets them a commendation. Meanwhile, using the information provided to him by Falsone, Lewis has had members of the Mahoney organization under surveillance. Is Lewis involved in these murders? Kellerman receives some good news for a change; passing a tape of his conversation with Judge Gibbons onto the FBI won't be necessary. The FBI is about ready to move with their case against Gibbons. The body count of the Mahoney organization rises to ten and we see that Lewis is near the scene.
Ballard and Gharty investigate the deaths of two single women who were bought drinks by a married couple. The victims were stunned and then strangled. The other detectives receive detailed information that helps them close the open Mahoney drug shootings. Their helpful informant turns out to be Lewis, who has a hearing coming up Ballard and Gharty get their suspect in the box and he claims to be the one to stun the victims, but his wife actually did the strangulation. Ballard is skeptical about the woman's involvement, but the evidence points to the couple.
Ballard and Munch catch a case involving the death of a prominent businesswoman. Pembleton and Bayliss catch a similar case. Both deaths might be the suicides they appear to be, but as the detectives begin their investigations the facts reveal otherwise. Lewis attends his disciplinary hearing and receives his punishment and is allowed to return to duty in the Homicide unit. Falsone and Lewis investigate another Mahoney related death. The situation within the Mahoney organization may be getting out of control as jury selection begins in the civil suit. The judge dismisses the civil suit, just as he told Kellerman tbat he would. Kellerman confronts him after the trial about the FBI's investigation in front of several witnesses. Bayliss joins Ballard for dinner and he reveals some of his secrets.
Bayliss suffers from a recurring dream about the Adena Watson, his first homicide case and one that remains unsolved. An elderly man comes to the Homicide unit to confess to Bayliss that his father had committed a murder 66 years ago. Falsone is assigned to the case, only the case file is missing and found to be in the possession of retired homicide detective, Thomas Finnegan. Gee allows Finnegan's request to participate in the reopened investigation. Questioning the elderly man leads to the recovery of the gun that might close the case. Falsone, Finnegan, Lewis and Kellerman celebrate their potential victory as Bayliss recontemplates the Watson case.
Judge Gibbons has been stabbed. On their way to the crime scene, Bayliss and Pembleton talk about a book that Bayliss is reading, then Pembleton wonders if anyone would ever write a book about their Homicide unit. A probation officer is murdered in a drive-by shooting. The FBI gets involved with investigation of the Gibbons death. Agent Bauer mentions to Bayliss that Kellerman's confrontation with Gibbons probably got the judge killed. He wants Kellerman clear of the case. A fingerprint lifted from the Gibbons' crime scene points to Georgia Rae's son, Junior Bunk. Falsone and Stivers get a lead on their probation officer shooting case. As Junior Bunk is brought in for questioning, he eyeballs a handgun being put in a drawer. Pembleton and Bayliss get Junior in the box and he is no longer able to be intimidated. While waiting to be transferred to central booking, Kellerman, Lewis & Gharty harass Junior. Slightly freed up to make a phone call, Junior gets the gun out of the desk and begins shooting. Gharty, Ballard and three uniforms are hit. Junior is killed in the crossfire from the guns of Gee, Bayliss, Lewis and Kellerman. Ballard and Gharty are in surgery as war is declared between the Baltimore PD and the Mahoney organization.
The search for Georgia Rae and the war against her organization begin. Stivers, uncomfortable with the whole situation tells Gee about the Luther Mahoney shooting. Ballard and Gharty begin to deal with their recovery. A lead on Georgia Rae's whereabouts is uncovered. During the assault on the building, Georgia Rae's body is found and Bayliss takes a bullet that would have hit Pembleton. Gee asks Pembleton to get to heart of the Luther Mahoney shooting that started it all. Pembleton and Falsone start with Lewis and then they move onto Kellerman. The truth about the shooting comes out and Kellerman claims sole responsibility, Pembleton asks him for his badge. To protect Stivers and Lewis from prosecution, Kellerman resigns. Feeling remorse for the hesitation that caused Bayliss to take a bullet for him and with Gee's plans to cover-up the truth about the Luther Mahoney shooting, Pembleton decides it is time to resign.
Bayliss returns to duty to discover the bosses have renovated the squad room in an attempt to make everyone forget the tragedy of last May. Gharty and Ballard have also returned and Ballard debates about whether she should ask Falsone to the Lodge party. New detective, Rene Sheppard, tells her just to go for it. Seizing the opportunity, Lewis goes for it and asks Sheppard to the party; it seems that he and Barbara have separated and are on their way to divorce. Meanwhile, Falsone speculates if he should ask Sheppard to the party. The first case Bayliss catches, now partnered with Munch, involves the dismembered body of Angelo Faltislo, a friend of Gee's cousin, Mario Giardello. Stivers and Falsone's case is similar: Leo Grimaldi, another friend of Mario, is also found dead. When Gee goes to question cousin Mario, he finds Mario's body in the same condition as that of his friends. Gee's estranged son, Mike Giardello, an FBI agent in Arizona, returns for the funeral. Mike asks Falsone (who initially declines) if he can help with the investigation. Mike discovers an old family secret is the key to the murders that key having just been released from prison. Mike's surveillance of the key's offspring reveals that they are involved and they are arrested. However, even with all the evidence -- nobody's talking; Danvers can only assure that two of the three murders can be closed with convictions; the Giardello case remains open. Mike and Gee work on reducing the strain in their relationship and Mike decides he is going to ask the FBI for a transfer that will get him back to Baltimore.
Sheppard and Lewis investigate the death of a man who has a twin brother. Gharty talks about wanting to live his life; he and Ballard go to the hospital to investigate the death of a teenager. Bayliss has interest in Sheppard; later he seeks advice from Stivers, who tells him to get in line behind Lewis and Falsone. Lewis and Sheppard interview the remaining twin and his mother; she confirms his story and they try to point to the dead twin's girlfriend. Meanwhile the friend of the teenage victim in Ballard and Gharty's case confesses that his friend wasn't shot in Baltimore, but rather D.C.; he drove his friend back to Baltimore so their parent's wouldn't "kill them" for buying drugs in D.C. Gee hopes to get the case moved to D.C. Mike Giardello puts in for his FBI transfer, but the only openings they have in the area are for liaisons to local police departments. He interviews with Gaffney, who is so open to the idea, he can't wait to tell Gee. That's something Mike was going to wait for the right moment to do. Ballard and Gharty can't get their case transferred to D.C.; instead, a D.C. cop, Landrewsky, joins their investigation -- although the victim's friend has given them little to go on. Lewis and Sheppard work on the surviving twin and his mother to try and break their case. Mike and his father discuss their new working relationship. Ballard, Gharty, Landrewsky and their witness drive around DC, hoping to trigger the witness's memory -- no luck there. Gharty mentions the fact that he's left Flora. Mike moves into his new workspace.
MGee (Mike Giardello) and Ballard investigate a double shooting at the home of a prominent sports doctor and his wife, a dermatologist. The doctor (who was wounded) did not realize the deceased (thought to be a prowler) was his sister-in-law. Munch contends with the IRS; his Waterfront partners want him to make sure that his cousin, their accountant, has been paying their taxes. The Waterfront needs a loan to pay for some improvements. Gharty has taken the day off, to take care of personal matters, like his recent separation from Flora. Munch has his hearing with the IRS; he owes $30,000 in back taxes. Bayliss and Sheppard discuss his sexuality and the possibility of a date. Falsone takes MGee and Ballard to meet an old fight man who knew their doctor. Ballard becomes excited while watching Falsone spar in the ring. MGee and Ballard's investigation lead them right back to the doctor's house, where his wife may be guilty of conspiracy to commit homicide. Gharty stops by the Waterfront to check on Billie Lou's availability.
A woman brings to the homicide unit her mystery-writer husband's videotaped declaration that his literary agent is responsible for his murder. Ballard and Gharty catch the case -- only there is no body or crime scene. Meanwhile, Munch and Bayliss investigate the death of an elderly woman that occurred during a break-in -- was it a homicide? Munch would rather leave for his weekend rendezvous with Billie Lou. Ballard and Gharty's investigation becomes a red-ball as they find evidence in the writer's office that a crime was committed. A break leads to the arrest of the literary agent and his accomplice, although Danvers can't guarantee a conviction. Falsone asks Ballard if she would like to go out Saturday night; just then the jury comes back. And a sharp-eyed juror insures that justice is done.
Ballard is annoyed when she finds out that the fact that she had a date with Falsone is around the squad room. Munch has a doctor's appointment and he's not talking about it. Dr. Griscom calls on the homicide unit when he sees a number of deaths that are related by a poison named phosphozine. The FBI steps in on the poisonings and they put MGee in charge of a task force; they consider it an act of domestic terrorism. One of the victims was a priest; two others were his parishioners. Gharty suspects the communion wine. Following this idea, wine bottles are collected from churches around the city. A needle hole is found through one of the corks. A citywide canvassing of all places where wine can be purchased is launched. Gee disagrees with the bureau's policy of keep information from the public. One possible suspect is captured; however, strange as he is, he's not the one. Through an internal leak, the media is alerted and warns the public, sparking chaos. MGee suspects the source of the media leak is his father and Gee doesn't deny it. Further investigations lead to a phosphozine delivery in which one bottle was allegedly damaged and discarded, the delivery driver (whom Bayliss & Sheppard had encountered) is arrested.
Bounty hunters shoot, killing the wrong man, as they enter a building where their fugitive---a man named Joe Errico---has shot at them (and subsequently gotten away). Gharty has vague memories of a drinking binge from the night before. Falsone and Stivers catch the bounty-hunter case. Sheppard, during her days with the fugitive squad, had dealings with the head bounty hunter. Gaffney stops Gee and MGee on their way in, Baltimore magazine wants to do a father and son piece, using the wine case as a focal point. Gee is not interested, especially about the use of the wine case. Gharty struggles as he tries to reconstruct the events of the night before. Munch is bothered by Gharty's stories of Vietnam and each grows to dislike the other - perhaps some competitiveness over Billie Lou is beginning to brew here. Bounty hunter P.J. Johnson, who was identified as the triggerman, is charged and placed in one of the holding cells, near some of his previously captured quarry. Within an hour his bail is posted. Ironically, the next day HE jumps bail. The other bounty hunters join with the homicide detectives in their attempt to locate the original target, Joe Errico, whom they suspect P.J. is still going after. When MGee & Lewis and bounty hunter Lichte are in pursuit of the suspects, they collide with an elderly couple. P.J. stops his pursuit to offer assistance as Errico gets away. Lewis appears to be critically injured.
Lewis is transported to the hospital, as is the passenger of the car that MGee hit. Gharty is worked up about women and finances, because he and Flora and their lawyers are going to be working out the financial details of their divorce. Gee however, Knoll is the only one who can get any information on the whereabouts of Errico from Errico's mother. She has promised to page Knoll when her son calls. (Joe Errico has gone south to Miami.) Knoll offers to pay the expenses of having homicide detectives go to Miami and work with him, but Gee declines that generous offer and sends his detectives separately. In Miami, Bayliss and MGee work with Knoll to capture Errico. Knoll offers to split the huge bounty with the homicide detectives, which they of course refuse. MGee decides that the best use for the bounty might be for the man whose wife had died from the injuries she sustained in the car accident.
Mike Kellerman's new vocation is private investigation, where the majority of the work involves catching cheating spouses. Falsone and Stivers catch a case where a newborn baby's body is found buried behind a motel. A young couple had checked into the room where the baby was delivered. The room was paid for using the girl's credit card. When they locate the girl (Debbie at home with her parents), she collapses and is brought to the hospital. The boy, Craig, is also located. Both say that the baby was stillborn; however, the autopsy reveals that the baby took a breath after it was born, so the death is ruled a homicide. Falsone notes that of the two, only the boy Craig seems to show any compassion for the baby. Kellerman meets Sheppard for a beer and tries to ask her about Falsone's baby case, later he asks around the squad room. Kellerman is hired to conduct his own investigation by the girl's defense team. Gee demands that Falsone and Stivers find convicting evidence before Kellerman finds anything. Kellerman advises his clients that their daughter needs to make a deal that convicts her boyfriend. They know that she won't do that, so they ask him to try to scare her into making the deal. The boy and girl stick to their story. Using a grand jury, Danvers plans to go for a manslaughter charge. While the jury is out Kellerman recommends to his clients that they don't post bail for their daughter, instead let her get a taste of what jail is like, maybe that will convince her to make a deal. The grand jury grants the indictments and bail is not posted, the boy and girl are sent to jail. A short time after being put into her cell, the girl calls her parents asking to be let out, saying, "Craig was the one that murdered IT."
Debbie Straub signs the plea agreement, pointing to Craig as the killer of the baby. Falsone wants more time to work on the case. Danvers reminds Kellerman there was a time when the truth mattered more than his paycheck. Gharty goes off when Sheppard and MGee ask to many questions about Kellerman's leaving of the homicide unit. Kellerman appears to begin doing the right thing, but doesn't pass anything on to anyone who might be able to do anything with it. Craig believes that Debbie isn't going to let him down and he has no plans to testify on his own behalf. Ballard searches for a dinner date when Falsone leaves a message he won't be joining her. When she sees him in the Waterfront later, she lets him know how she feels about his method of communication. The case goes to trial, Debbie testifies that Craig killed the baby; with no evidence to the contrary, the jury finds Craig guilty. Falsone talks with Craig about what really happened; however, it is all to no avail as the following morning Craig hangs himself, literally. Later that day, Falsone receives an "anonymous" tip with recorded messages from Debbie to Craig; unfortunately, Danvers says the information isn't going to do them any good at this point of the case. Kellerman and Falsone make some sort of peace with each other.
A white bus driver striking a black female pedestrian sparks a riot. The driver is killed, and some distance away from the riot another body is found. MGee and Gharty look into the death of the driver while Lewis and Sheppard look into death of the other body. Lewis finds a clue at the scene, a button (later discovered to be missing from a police uniform). Gharty and MGee actively debate whether race was the motivation for the driver's beating death; MGee suspects the incident wasn't racially motivated. The bus riders are interviewed to find out what they know. Lewis and Sheppard approach a house looking for their witness (without backup). For her trouble Sheppard keeps hold of her suspect, but loses her gun and is severely beaten. Ballard is recalled from her hiking vacation. Lewis lays down the law for the residents of "Little Jamaica"; he wants Sheppard's gun returned tonight. The witness Sheppard caught identifies Hellriegel as the murderer, and the men who beat the driver to death are also identified. The gun is returned.
A body buried for 6 - 20 years is uncovered at a construction site. Munch and Lewis begin the process of trying to solve this old crime. Falsone and Ballard's relationship has heated up, and that fact becomes apparent to their fellow detectives. Sheppard returns to work, but is discouraged when Gee assigns her to desk duty. Gharty tells Billie Lou that he'll attend her bass-playing concert. Munch they agree.
Gharty has a Vietnam flashback. Sheppard is placed back into rotation. Lewis asks Falsone to switch cases, as Lewis is still unsure about Sheppard's ability to be back on the street in the part of town where their call lies. Munch and MGee work a case where the victim was hit and run. One of the victim's possessions is a knife that has some meaning for Gharty, who later is able to recognize the tattoo found on the victim. Sheppard confronts Lewis about the case switch. She and Stivers talk more... after Stivers, working with Falsone, sees him "go off" on a potential witness... Munch and MGee find their hit and run vehicle, a rental SUV, whose renter claims to know nothing of the incident and says he had filed a stolen-vehicle report. Munch pulls the victim's DOD file and---for good measure---Gharty's! Munch, begins to spread doubts with the other detectives about Gharty's Vietnam experience, because the file tells him that Gharty had a less than honorable discharge. A kid, who had stolen the SUV, comes forward with his mother apologizing for the hit and run. When Ballard asks Gharty about Vietnam and mentions Munch's name, Gharty goes to the Waterfront to confront Munch. In the ensuing confrontation, Billie Lou's bass playing hand is injured; then Gharty tells his Vietnam story.
The Internet is stage for a ritual murder, which was staged -- which was staged, or was it? The body is found the following morning and Sheppard takes the call, her first since the beating. Since Lewis can't be found, she partners with Bayliss. Second shift detectives Bonaventura and Austin catch word of the day shift's case. It seems the victim in Sheppard's case was a witness they had interviewed the day before about an online murder hoax. The detectives are informed about another murder that is scheduled for midnight. It's a red ball. The detectives try to put the clues together, but come up with nothing and must wait until the netcast begins before they can trace the killer. The trace is successful, but when they arrive at the scene, the killer has left them a computer with the words "Ha Ha Fooled You." Barnfather wants Bayliss reassigned as primary if something doesn't turn up soon. Sheppard goes online to flush out the killer. He advertises another murder will take place at www.inplainsite.com, which turns out to be a web site run by Bayliss. The webcast begins, the killer's cell phone signal is tracked and he is apprehended.
Ballard and Bayliss are called to the scene of the mysterious death of a woman, whose body is found at the bottom of a forty-foot cliff. This victim was to be married the following morning. The two detectives work to determine whether the death was accidental or intentional (via murder or suicide). Meanwhile Sheppard and MGee begin investigating the death of a movie patron, whose body was discovered after the show ended and the theater cleared out. MGee mentions to Sheppard that his sister is about to have a baby, which means Gee is about to become a grandfather. Their investigation reveals that the movie patron was regularly loud and obnoxious and thus bad for business. When an overdose of a sedative is found in his bloodstream, the detectives question the theater owner, who was currently in litigation with the victim. Unfortunately for Ballard and Bayliss, their case remains unsolved.
Danvers brings news of his appointment to the District Court bench as the investigation of a government official named Janine McBride, begun on Law but neither the Independent Counsel nor McCoy and Danvers get anything useful. Meanwhile, the Baltimore detectives investigate the background of Chesley Purcell and it turns up the name of a man in prison who still appears to be running his organization. So there could be no more leaks, MGee asks to be kept out of the investigation. Munch and Sheppard question Walter Boyce, the prisoner who arranged the hit on McBride. Lewis is still worried about Sheppard's ability to perform on the street and Stivers is still trying to "get right" with Sheppard's actions during the incident where Sheppard was beaten up. Boyce is to be rewarded by someone with connections at the White House. Danvers appeals to the judge to do the right thing and deny Boyce the hearing that may get him released from prison early. Walter Dawkins, who is located in the White House, denies having any knowledge of Boyce. MGee finds information that McBride, the original victim in this case, was going to be a witness in Dell's investigation. When all the facts come together, it's Danvers and McCoy who believe they will be able to subpoena Dell to testify in their case. The Independent Counsel has information on Danvers' past, and Danvers appeals to Gee and the Baltimore CID for help. For Danvers it means he will probably lose approval of his judgeship. All the hard work of the Baltimore and New York detectives and attorneys only helps Dell to get the witness he needs to continue going after the Administration.
A woman comes looking for Falsone, knowing that he solved a real old case, wants him to look into a case for her from 1972. Her parents told her that she was responsible for her younger brother's death. Despite being three years old at the time, the woman has doubts about her parents' story. So Falsone and Stivers reopen this case, which was closed by Gee when he was a new detective. The reopening of the case makes Gee think that he may not have been totally focused on the case at the time. Their investigation reveals the woman's mother used her as a scapegoat for the mother's crime. Bayliss and Ballard's case involves a body that was shot, but the victim was already dead from a drug overdose. The male sergeant at the scene piques Bayliss's interest, so they get together for drinks. Their relationship doesn't develop, because word is spreading about Bayliss being the owner of the "In Plain Site" web site. Bayliss begins feeling pressure about his being different and considers celibacy. Ballard may consider the same option, when her relationship with Falsone becomes difficult to maintain as a secret.
Lewis and Munch begin to investigate the death of a Buddhist monk beaten to death. Lewis isn't interested in working the case with Bayliss, whom he feels, may become too emotionally involved. Ballard and Falsone agree to call their relationship quits. Ballard and Gharty's case involves a man who was shot down in the street; the three witnesses that saw the shooter all have different recollections of his appearance. As a result, their prime suspect cannot be charged. Gee asks for Bayliss's assistance in the Buddhist murder and to Lewis's dismay, Munch abdicates his position in the investigation to Bayliss. Lewis and Bayliss take different approaches to the investigation. Bayliss's approach leads him to the man who committed the crime, but cornering his suspect leads to a showdown with guns and Bayliss fires a fatal shot. Later Bayliss tries to reconcile the shooting with his own feelings about being a Buddhist and being a cop.
In Stivers and Falsone's case, a man is found shot dead in his bed, with no signs of a struggle. Gee lobbies Barnfather to find a way to get them the ability to have some control over their FBI liaison, so they don't experience the same problems they had with the Janine McBride case. Barnfather lets Gee know that there is Captain's position opening up and he should be inline for it with no catches. Lewis lets Ballard accompany him on a bar stabbing, when she accuses him of being afraid to work with a female, since the incident with Sheppard. While she does get to help him with the initial investigation, Lewis manages to work the rest of the case on his own, leaving her to handle the details. Meanwhile, Ballard's usual partner Gharty spends a "mental health day" at the Waterfront Bar, drinking and proposing to Billie Lou. Stivers and Falsone discover their victim had a bad breakup with his ex-wife Eleanor Burke, and she admits to committing the crime; however, as an assistant US attorney, she plan's on using "Battered Spouse Syndrome" as the defense that will let her plead this as a case of self-defense. Ironic since the victim showed no signs of struggle. Falsone follows Ballard, when he finds out that she has joined the ME's duckpin bowling team. The judge on the murder case feels that no one is speaking for the victim, since Danvers seems to be doing little to prosecute, so he sets the bail high. Danvers asks Gee to talk with the judge, who he knows is an old friend of Gees, to see if he can't get him to change his ruling. Gee understands where the judge is coming from and makes a stand on it that Barnfather thinks is not politically correct for Gee's pending promotion. MGee reveals evidence he had in his possession that implicates Burke in her crime, that he was holding back because of pressures he was getting regarding his father's possible promotion. The charges are upgraded to 2nd degree murder.
Falsone and Lewis investigate the murder of a man in his own backyard. The victim's nose was removed from his body. Ballard and Gharty investigate the murder of a bartender at a strip club. Canvassing the neighbors, Falsone feels that one of the neighbors isn't what she appears to be. Later when they interview her husband, he gets the same feeling. The MEs complete a record setting day of completing autopsies, but find themselves with one unidentified extra body. Munch and Bayliss get the call, but insist that until they can get a crime scene to go to, the problem isn't theirs. Griscom finds the crime scene in the morgue freezer. Ballard mentions to Gharty that he might want to consider stopping his drinking. Falsone's theory about the victim's neighbors proves true when MGee checks into the Witness Protection program. MGee's phone call puts the wheels in motion to get the family moved. Falsone and Lewis arrive just in time to take their suspect into custody and away from the Feds. The suspect in Ballard and Gharty's case is a transvestite hooker who isn't very smart. Gharty decides to follow Ballard's suggestion to stop drinking for a month. MGee feels betrayed by the Bureau and decides that his only choice is resignation.
Emmet Carey is holding his two children hostage in the apartment of his wife's sister. He sees MGee on television and decides that he will talk only to him and occasionally Gharty who is also on the scene. The wife also shows up on the scene and gets past the security. Her screaming sets of Emmet, who fires two shots out that window that strike his wife dead. MGee has to keep the information from him as they continue to negotiate. The crisis ends when Emmet releases his stepdaughter, but makes a deadly choice for himself and his son.
When the men are nowhere to be found, Sheppard and Ballard team up to investigate the death of young girl, who's a teenage gang member. With the wedding one week away, Billie Lou asks for Munch's help with her neighbor's abusive boyfriend. After Munch approaches him strongly, the boyfriend retaliates by coming to the Waterfront and slamming Billie Lou's head on the bar. Munch claims he came on strong with the guy, because his "testosterone riddled behavior" was due to the celibacy Billie Lou imposed on him, to make their wedding night more special. Billie Lou wants to delay the wedding until the welt on her forehead goes away in about 3 weeks. After Sheppard and Ballard solve their case, Sheppard reminds Lewis that his problem with her is not going to keep her from doing her job.
Sheppard and Bayliss await the trial of Luke Ryland, the Internet killer. A number of delays keep the hearing from being held; the last time it is because Danvers can't make it due to being held up in another trial. Because of a technicality in the law, Ryland is set free. Bayliss is outraged and winds up pushing Danvers, who later threatens to put Bayliss up on charges. Gee's daughter Teresa arrives, to help with the celebration of her father's promotion. Gee asks Bayliss to apologize to Danvers and Bayliss declines. Lewis and Falsone look into the murder of a drug addict whose husband looks like the most probable suspect. The victim's mother-in-law isn't very cooperative and her sister is a nun who thinks her brother-in-law is an architect. Gee worries about whether or not he will be able to perform in his new role as Captain of the property crimes division, later he turns down the promotion. Bayliss and Lewis have words about the way each other handle their memories of the past. Munch and Billie Lou get married, with Gee and Ballard as the witnesses; however, Munch's six weeks of celibacy result in a "premature" end to the wedding night activities. The drug addict's husband is found, questioned and charged; the nun asks to see her brother-in-law, so that she may forgive him for his actions. Lewis reconsiders his position on Sheppard, when his comment about the nun's ability for forgiveness and Falsone's response gets him thinking. Bayliss warns Luke Ryland that he'll be watching him. Ryland says he is leaving town, but Bayliss can always find him on the Internet. Bayliss talks with Munch about Gordon Pratt (the man who shot Bolander, Howard and Felton) and confesses to Munch that he once suspected that Munch might have been the one to kill Pratt. Bayliss also goes to visit Danvers and apologizes. Lewis asks Sheppard to partner with him on a case. Bayliss packs up his things and quietly leaves the Homicide unit. The body found is Luke Ryland's.