Simone and Sipowicz get another case involving the shooting of a rap artist who refuses to cooperate with them in the identification of his assailant. Meanwhile, Abby tells Medavoy that she and Kathy are trying to start a family and asks him to donate his sperm to her so Abby will get pregnant. Officer Szymanski, the racist cop who pulled over Fancy, tells him that he thinks Fancy was one of the ones responsible for his being set-up and caught in the alleged theft of a drug dealer's money. Also, Simone is approached and propositioned by FBI agents to help them with their ongoing investigation into the affairs of mobster Joey Salvo. Elsewhere, the night shift detective, Vince Gotelli, tells Simone and Sipowicz about a heart medical condition of his.

An inebriated Vince Gotelli is arrested after "hijacking" a city bus and having it wrecked. Fancy meets with the bus driver's boss to work out an arrangement about their investigation and suggests that Gotelli take some medical treatment. But it takes a forced intervention by Martinez, Medavoy, and Russell to convince Gotelli to get medical and psychiatric help in which Gotelli decides to throw in his badge for good. Meanwhile, Simone's continuing help with the FBI makes his life miserable when the men from Internal Affairs investigate him for the government license plate number on Salvo's car that he ran and is frustrated when he cannot tell them, not even Sipowicz, about what he's doing. Elsewhere, Sipowicz and Simone investigate the beating and murder of a woman in her apartment and deal with the emotionally sensate superintendent of the building whom they think he knows more than he's telling them.

Simone's continued involvement with the FBI sting against Joey Salvo jeopardizes his career when the men from Internal Affairs investigate him and suspend him from active duty. Meanwhile, Sipowicz and Russell investigate the gruesome murder of a young woman where a psychiatrist, named Dr. Wentzel, insists on implicating his patient's father for her murder. Martinez and Medavoy have a hard time over a haughty mugging victim who is a writer from a local magazine that wrote a bad story on the cops of New York City. Simone's involvement with the FBI reaches a cliff-hanging climax when in a secret meeting with Salvo, the mobster is hit by gunfire by an unseen assassin. Sipowitz, following Simone, comes on the scene and sees Simone standing over Salvo's dead body... and thinks Simone killed him!

In the four months since Joey Salvo's assassination, Simone is working odd jobs since he has been suspended by Internal Affairs pending their investigation, while he approaches Sipowicz asking about his and others incitements by the FBI who think that Salvo's death was an inside job within IAB, and Lt. Shannon from IAB tells Lt. Fancy that he may know the person who killed Salvo. Meanwhile, Gina discovers herself to be pregnant, but is hesitant on telling Martinez.