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 and Lewis investigate the shooting of a fellow police officer whom Crosetti regards as a son, Howard suspects a rabid Spiro Agnew fan of murder but ends up solving the Calpurnia Church case meanwhile Bolander makes a friend whose death interrupts his date with Dr. Blythe.

Crosetti focuses his investigation into the shooting of Officer Thormann on one suspect, while Lewis continues to investigate. Meanwhile, Pembleton and Bayliss pursue different leads in the murder case of eleven-year-old Adena Watson.

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

While Giardello is busy sending off an old friend to retirement Pembleton and Bayliss investigate the murder of a dog, Howard and Felton argue over whether Felton finds Howard attractive while dealing with a drug-related homicide and Bolander and Munch take Dr. Blythe's son on a ride along. Meanwhile, Crosetti takes care of the bed-ridden and blind Thormann.

Howard and Felton are in court over the Pony Johnson case, Crosetti and Lewis go head to head with the Secret Service and Bolander and Munch argue over drug legalization. Meanwhile, Pembleton gets an unexpected job offer.

Quitting smoking dominates the conversation ad behavior of the homicide detectives even as they solve what may be a gang-related killing of a 14-year-old boy. Lt. Giardello discovers a secret asbestos removal project on the third floor and confronts his superiors on behalf of his squad.

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.

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, must both 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.