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.

Just days after Sylvia gives birth to a baby boy (Theo), Sipowicz suffers an emotional setback when Andy Jr. is found murdered in the line of duty. Sipowicz wants Simone to lead the case of his son's killer and also wants the opportunity for restitution. With Russell in tow, Simone tries to balance his desire for revenge, as well as his quest for justice to catch the killers. While Sipowicz breaks the news of his son's death to his first wife, Katie, he begins to show signs of an emotional breakdown. In the midst of all this turmoil, Donna makes her decision when she quits her job as administrative assistant to the precinct and moves to California, leaving New York for good.