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.

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.

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.

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.

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.

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.