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.

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.

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.

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.

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.""

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.

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.

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.

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 m

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 stol

Pembleton and Bayliss have only twelve hours to grill their prime suspect in the Adena Watson case before they must let him go.

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.

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

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.

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.

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.

The homicide team pulls the graveyard shift on the hottest night of the year. Bayliss is consumed by the Adena Watson case, driving a bigger wedge between him and partner Pembleton. Giardello finds a baby in a cage. A renegade Santa Claus runs loose in the building and the whole squad tries to figure out who's responsible for a candle that keeps getting lit.

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.

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.

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.