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.

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.

Sipowicz's AA sponsor, Danny Breen, is beaten up by his estranged son. Meanwhile, Simone and Sipowicz investigate the murder of a pregnant woman whose charred body leaves few clues. Martinez and Medavoy check out the story of a man who might have information about a pawn shop robbery.

Simone and Sipowicz investigate the murder of a gay bar owner during the Christmas holidays. Meanwhile, Fancy's wife goes into labor to have her baby. Breen breaks his promise to Sipowicz by checking up on his son and decides to go back to him, which turns out to be fatal when Breen's son kills him and Sipowicz has to arrest him.