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.

Kelly gets an ultra-high priced mob attorney to defend Janice on the double murder charges and helps out with her bail. Meanwhile, Sipowicz tries to make amends with Sylvia who's been attending Alanon meetings. While helping with Andy Jr. look for a new car, Sipowicz comes across a lead in a disappearance case that has frustrated him for the last 2 1/2 years. An old Ford van which may have been used in an abduction re-surfaces at the lot. Elsewhere, Kelly investigates the murder of a priest and later meets with Robin for a lunch date and spends the night with her.

Janice's murder trial begins, where Kelly risks the consequences when he testifies on Janice's behalf about their brief affair which results in the Internal Affairs Bureau investigating him. Meanwhile, Sipowicz works with an abused woman who's reluctant to testify against her husband. Medavoy, Martinez, Sipowicz and Kelly investigate robberies of drug dealers in their apartments. Sipowicz's AA sponsor wants him to agree to abide by a contract before he lets him try to restart his relationship with Sylvia. Donna tries to give Medavoy advice about dealing with his divorce. Also, Robin leaves Kelly for good when he tells her that he still has feelings for Janice.

Internal Affairs begins to investigate Kelly and Sipowicz's arresting of the officers they caught robbing drug dealer's apartments, then they begin looking into Kelly's handling of the notebook that was part of Medavoy's case. Janice's murder trial continues where she takes the witness stand to give an emotional testimony about her reluctant involvement with the mob and is sent to prison with a two-year sentence. Meanwhile, Kelly and Sipowicz investigate a double murder.

John Irvin fears the worst when Dolores disappears. The detectives search for a body when a mentally ill man confesses to raping and murdering his girlfriend's daughter. Two brothers run their own investigation when their sibling is murdered.

Mike Roberts is found dead. John reveals a connection between Roberts and Cullinan, who was with Dolores when she died. Mike left behind a memoir detailing some of his work. Jill goes undercover as a drug-addicted hooker.

ADA Costas prepares for the trial against Cullinan, and chooses Sorenson to testify over her husband. A man is shot dead in his apartment, and his wife's story about Latinos looking for drugs doesn't add up.

Tensions mount as the Cullinan trial approaches. Mike Shannon brings a problem to Sorenson. Danny kisses Diane. There's a shooting at the courthouse.

The detectives investigate the shooting death of a man whose brother is a registered sex offender; and when Captain Fraker's trial gets underway, Sipowicz worries that his own testimony may have harmed the prosecution's case.

Sipowicz and Clark investigate the death of a transvestite whom a friend insists was having a relationship with a married man; a surgeon's hand is badly cut during a robbery; and Rodriguez testifies in the Fraker trial.

The detectives search for clues when a group of perpetrators torture a man for no apparent reason; a woman reports her husband as missing, but Sipowicz and Clark suspect she's not being completely forthcoming; and Fraker testifies in court.

The detectives investigate the strangulation death of a former porn star; a thirteen-year-old boy holds the key in implicating his father in his mother's murder; and the jury reaches a verdict in the Captain Fraker trial.