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.

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.

Sylvia confronts Sipowicz about her suspicions that he is going to late-night bars and drinking again, and the effect is everywhere. Lt. Fancy is forced to sent him home after Sipowicz walks in one morning drunk. Sipowicz even fights with some street punks, gets beaten up, and Simone offers to look for the men that beat Sipowicz up. Meanwhile, a new administrative assistant, named Lucy, arrives as Donna's replacement. Also, Russell investigates a young woman, named Angela, who claims to have been stabbed by her jealous boyfriend. Simone, following a lead from a streetwalker named Deena, finally tracks down and confronts the two thugs who murdered Andy Jr. and guns them both down in a hail of bullets.

The detectives get a break in a case involving a police officer suspected of committing murder.

As Sipowicz prepares for prostate surgery with Sylvia by his side, James Martinez returns after recovering from his back problem where he reports that Gina had her baby three weeks earlier. But Medavoy is even happier after returning from upstate New York with a videotape of Abby giving birth to her baby and is very eager to show the tape to anyone who will watch. Meanwhile, the rest of the squad gets involved in a case of five reuniting Army buddies when one of them is found dead. The four others try to keep their fabricated story straight as Simone and the others try to figure out their involvement.

A murdered couple is found where the dead man is a car salesman and the woman is a prostitute. Simone and Sipowicz look into the salesman's death, while Medavoy and the other detectives look into the prostitute's death, where the M.O. of the suspect is to buy used condoms from a prostitute and then mix the spent semen with his own to cover his crime. As Sipowicz recovers from his surgery, he finds that a recent blood test is not favorable and once again keeps his medical problem to himself.

Simone and Sipowicz work with Cohen to investigate the death of one of Cohen's witnesses and her son. Evidence points to the opposing attorney having some involvement with the arrangement of the homicide. Meanwhile, Russell and Kirkendall try to help a man locate his missing daughter. Medavoy and Martinez look into a corporation dealing with fake sports memorabilia, where Medavoy is taken in with the blond employees who reminds him of the departed Donna. Also, when Sipowicz thinks about his low sexual functions, his doctor prescribes the wonder drug Viagra. In the mist of all the cases, Simone and Russell decide to get married on their lunch break, but their cases get in the way of it all.