Lesniak deals with a perpetrator and his "high priced lawyer and shrink" when he repeats the offense. Meanwhile, Detective Solomon uses a fast pull to take a possible serial killer case away from Simone after he brings in a possible suspect. One of Fancy's old contacts, Vinnie Greco, brings in a tip about a couple of guys looking for some heavy arms to do an armored car job and Sipowicz works with him, but Greco is working for someone else against Fancy. Sipowicz invites Andy Jr. over at his place for dinner where his son tells him that he is joining the Air Force. Also, Sipowicz proposes marriage to Sylvia and this time, she accepts.

After discovering a key piece of evidence, Simone gets his chance by Detective Archie Solomon to question the serial killer suspect George Putnam. Meanwhile, Sipowicz, Medavoy and others work on how to stop the armored car robbery and Fancy has a confrontation with Haverill about using his informant, Vinny, as a pawn to try to bring him down and plays a tape for Haverill which he reveals his true attitude which results in his resignation as the zone commander. Also, Martinez and Lesniak arrest an odd extortionist, while romantic feelings for each other begin to appear, and Simone also develops romantic feelings for his writer friend Benita Alden.

Simone and Sipowicz collide in their squad car with a Romanian immigrant who has a woman locked in the trunk of his car and later, their investigation shows him to be a possible terrorist and holding a wealthy family prisoner with pipe bombs. Meanwhile, the serial killer, George Putnam is shot by an unknown sniper. Simone begins to investigate the father of the killer's last victim, Mr. Rudman, and another member of a victim's support group... who all appear to be part of a secret vigilante group. Medavoy talks to Dana about his relationship with Donna if he's losing interest in her, but the crafty Dana takes advantage of the situation to try to break them up by playing on his mental neurosis as the cause of Donna's lack of trust in Medavoy. Also, Martinez keeps asking Lesniak to go out on a date with him.

Simone and Sipowicz search for a killer following a shooting spree, which left several people dead and where a rookie cop's missed shot also killed a bystander. Meanwhile, Fancy's younger brother, Reginald, a policeman in the 8th precinct, has racial troubles with his commanding officer and Fancy intercedes on his behalf and his own boss, Captain Bass, covers for him. Sipowicz sees a doctor and discovers he has an enlarged prostate and Sylvia mistakenly thinks their lack of sexual activity over the past few weeks was because of the rape incident from her past that she told him about.

Martinez is shot in the back during a scuffle and the doctor's report is possible that he may be paralyzed for life. But Martinez's assailant, a government witness in a relocation program, will probably go free and Simone contacts reporter Benita Alden, his former girlfriend, to help put pressure on the D.A. to prosecute their protected witness. Meanwhile, Russell, on the road to recovery from her alcoholism, wants Sipowicz to let Simone know she's doing okay but she is on the brink of falling off the wagon. Donna expresses to Simone that she has feelings for him, and Sylvia tells Sipowicz that she may be pregnant.

Sipowicz becomes annoyed when federal agents take over their investigation of the disappearance of a millionaire. Then a petty criminal from the past surfaces with information about the kidnapping and Sipowicz decides to act on it. Meanwhile, Simone aids an old boxer friend of his, who happened to got him started with bird breeding.

Sipowicz has race relation problems with the organizer of a local basketball game, held in the memory of a young boy, which erupted into violence by the gang members on the opposing sides which left two dead and seven wounded, and was witnessed by a reporter. Fancy has problems when Sipowicz racist colors come to light and has him removed from the case, much to his anger.

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.