A group of detectives and officers work at the 15th Precinct, a seedy police station in Manhattan, New York City. Detective John Kelly, a 15-year veteran of the force, deals with his partner Andy Sipowitz, an alcoholic 20-year veteran detective. Laura Michaels, an aspiring lawyer and Detective Kelly's wife, is having problems with their marriage and she hires Josh Goldstein, a lawyer who lives in apartment 4B of their building to work on a divorce, who gets mugged in the laundry room of the building. Meanwhile, Sipowicz is relentlessly pursuing mobster Alfonse Giardella, who threatens Sipowicz to leave him alone. Later, Sipowicz is shot by Giardella during a tryst with a prostitute. Enraged, Kelly orders the precinct officers to hound Giardella and his ruthless employer; mafia kingpin Angelo Marino. The new patrol officer, Janice Licalsi, is attracted to Detective Kelly. But is she is revealed to be an informant for Marino who orders her to murder Kelly.

Inspector Lastarza of the Organized Crime Unit tells Lt. Fancy and Kelly that they stop applying pressure to the local mob for their pursuit of Angelo Marino is hurting the FBI investigation to nail Marino. Meanwhile, Sipowicz regains consciousness in the hospital after the shooting, but he has no memory about the attempt on his life because he was drunk at the time. Laura and John Kelly become officially separated and she decides to join a private law firm. Josh "4B" Goldstein becomes more paranoid about his mugging and brings a gun into the laundry room every night in hopes to catch his attacker. Kelly tries to reason with a deranged man who has taken a judge hostage who let his son's killer free. Elsewhere, Angelo Marino puts more pressure on Janice to murder Kelly, but she kills him and his chauffeur/bodyguard instead and slips away.

Sipowicz has a cavity and decides to have it taken care of by his son's dentist. At the dental office, Sipowitz finds himself unsuccessfully trying to prevent the suicidal Dr. Fleishman from jumping off a 28th floor ledge. Meanwhile, Medavoy and Martinez work on a strangulation murder case that appears to be the work of a cross-dresser. LaSalle's first case for the squad involves a woman who was raped and she, Kelly, Sipowicz try to catch the most probable suspect. Janice joins the undercover squad and is partnered with the hot-tempered Roy Larson to assist with LaSalle's case, while Sipowicz suspects that Larson's short temper and odd behavior points to a drug problem. Also, Lois Snyder (the prostitute who set Sipowicz to be shot in the premiere episode) returns to try to apologize to him about the incident and also wants to renew their romance. But Sipowicz turns her down and goes back to start whatever relationship she has with D.A. Sylvia Costas.

Martinez investigates a baby that was killed in a car from an apparent drive-by shooting. Meanwhile, Lois Snyder contacts Sipowicz for help because a policeman that she was entertaining died in a compromising position and he moves the body to a less conspicuous location. Lesniak's ex-boyfriend, Officer Abruzzo, keeps showing up at the precinct and harassing her, while at the same time, Lesniak locks horns with the officious Vince Gotelli over his working skills and his racy items he keeps. Kelly's future with the department is decided when Internal Affairs comes to the precinct to re-investigate some of his old cases and the result is Haverill transferring Kelly to borough dispatch duty. But Kelly decides to quit the force and after saying goodbye to Sipowitz, he throws in his badge for good.