Simone deals with an emotionally fragile woman, named Joyce Novak, whom is a witness for a double-murder when she keeps changing her story, for she is really only interested in flirting with him. Meanwhile, Sipowicz participates in the investigation where a family-run business, that he used to work in, is held up and the owner's wife is killed. After Donna leaves town for a long vacation (and to get away from the annoying Medavoy), her temporary replacement, John Irvin, is a flamboyantly gay man whom Simone used to know from his old precinct. But Irvin makes the whole the station, including the bigoted Sipowitz, uncomfortable. Also, Martinez enters in a police department boxing tournament.

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.

Rodriguez mediates when Sipowicz and Sorenson clash with detectives from another squad anxious to solve a multiple murder case; Medavoy and Jones try their hand at making extra cash by cleaning up murder scenes.