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.

After Israel hangs himself, Sipowicz investigates a clue which is a bible verse that Israel pointed out to him, which leads Sipowicz and Simone to set up a complex sting operation to find out if the father of the murdered boy really was the one that set the whole Israel frame-up. Meanwhile, Medavoy and Martinez look into a doctor who is helping out the homeless by getting them a job with insurance benefits that he helps collect.

Sorenson and Sipowicz investigate the murder of a nine-year-old girl whose body was discovered inside a locked basement. Medavoy and Martinez assist an elderly man who believes that his young girlfriend was pressured into embezzling money from him.

The temperature is rising. Sipowicz receives a death threat. A prostitute is murdered, causing IA to look at Clark. A huge drugs and cash hoard is found. An elderly woman is found tied up and beaten.

A man armed with a bomb walks into the station house and handcuffs himself to McDowell; unless the detectives release a Russian mobster from jail in one hour, the bomb will detonate.

The detectives investigate the smothering death of an elderly man married to a voluptuous woman in her 20s; and a state judge pressures Medavoy and Jones to find out who poisoned her mother.

Detective John Clark Jr., Andy Sipowicz (who just was promoted Sergeant) and a military investigator examine the murder of military recruiter Sergeant Lester Bakewell, whose affair with a female colleague caused her divorce from a retired veteran Colonel; however, the prime suspect is student Paul Corbelli, whose brother was killed in service in Iraq. A woman reports her homeless Basque uncle missing abnormally since four days; he's found dead and Detectives Baldwin Jones and Greg Medavoy investigate.