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.

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.

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.

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.