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As he begins his new job as squad commander, Sipowicz disobeys orders and keeps a murder investigation open... even though a Japanese man with diplomatic immunity has confessed to the crime.

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.

Sipowicz helps his ex-wife deal with a drunk-driving violation. Simone's body rapidly succumbs to infection in the wake of his heart transplant.

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.

When another woman is murdered by the serial killer, the detectives arrest a suspect... and discover the killer's identity; and expecting a baby, Sipowicz and McDowell decide to get married.

Bale offers to recommend Sipowicz for the squad commander position; Ortiz and Murphy investigates the death of a Muslim woman; and detectives search for the man who shot Bale. Medavoy retires.

While investigating the murders of four teenage girls, the 15th squad discovers the shocking truth about the disappearance of detective Danny Sorenson.

Simone and Sipowicz investigate the disappearance of a young boy, who turns up dead and the father points that a mute homeless man, named Israel, may have been the one. But Supowicz suspects that the father may be the real culprit. Meanwhile, the rest of the squad investigate the murder of a Hasidic Jewish girl and have to juggle the need for their investigation against the needs for a quick burial.

Sipowicz is taken hostage in an interrogation room by a suspect in the murder of a pot dealer and two of her friends; a suburban mom found with drugs in her purse appears to be covering for her son.

Andy and Theo struggle to live without Sylvia, and the squad worries about them. Cullinan is confronted with new information about Mike's death. John is released from hospital.

While investigating a random stabbing, Sipowicz becomes obsessed with his own mortality after he's nearly gunned down by a murder suspect; Medavoy takes a job as a bouncer.

A meek and mousy young woman is found beaten to death. Her brother-in-law is very upset but not about her death--he was paying her money to use her apartment for an extramarital affair. Andy has Diane help with his custody case.

A squad member is shot while storming an apartment; Clark and Jones investigate the bludgeoning death of a woman whose wealthy husband was going to finance a friend's salon business.

The squad investigates the murder of a young Chinese girl along with an alleged rape case. Irvin learns his father is dying. Clark tries to find a foster home for James Kilik.

Andy's off-duty and slightly underhanded work to prove that Hatcher killed his own wife lands him a transfer out of the 15th precinct and into the Bellevue Morgue engineered by Detective Hatcher. Meanwhile, the squad is up to their whips and chains after a dominatrix is found murdered.

Sipowicz and Clark investigate when Julian Pisano is wounded in a shooting incident; McDowell and Ortiz assist a woman who doggedly pursues justice when she's conned out of $100; Clark grows concerned when his father stops returning his phone calls.

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. Andy has his promotion ceremony.

The detectives continue their search for a serial killer who targets alcoholics trying to get sober; and Clark and Jones investigate a homicide linked to a woman with whom Clark had a one-night stand.

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.

A man is suspected of killing minorities to avenge injuries his brother suffered during the first Gulf War; Sipowicz and McDowell plan to marry. Rita gets jealous over Clark's new ladyfriend.

The detectives investigate a grisly murder in which an elderly woman's hands and feet were cut off. Simone's health continues to deteriorate.

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 send 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.

Sorenson is missing, and a stripper is found murdered in his apartment. Medavoy and Jones investigate a killing, but the suspect identified by an eyewitness has a seemingly unshakable alibi.

Clark is placed under arrest after police find heroin in his car; detectives search for clues when a woman is beaten to death with a cordless drill; a murder victim's obsession with clean living may have led to his demise.

While investigating a murder, Sipowicz discovers a secret about Bale; and Ortiz and Murphy investigate a shooting tied to a talented up-and-coming basketball player.