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.

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.