The precinct's new C.O. alienates the squad with his hyper-controlling style of command; Ortiz's new partner is a flirtatious rookie; after the the suicide of his former girlfriend, Clark numbs the pain by drinking and womanizing; someone stalks Sipowicz.
Sipowicz is reprimanded by Lt. Bale; the ringleaders of an adoption scam may be responsible for the murder of a pregnant woman; detectives investigate claims by the wife of an ex-con that she was beaten and robbed by an intruder.
Sipowicz's son is kidnapped, and a reformed sex offender is found murdered.
A boy is held for ransom and a young woman is found dead in her apartment closet. Clark's testemony in a trial is treatened and he gets into a disagreement with Sipowicz.
A listening device planted in Sipowicz's car leads to him being shot while helping Clark home from a bar.
Medavoy takes a part-time job as security at a bar, an antique dealer reports a theft, and a thief knifes a father in front of his family on a bus.
Clark and Sipowicz make peace with each other; Clark protects an assaulted murder witness.
Clark continues to safeguard a witness as Jones is blamed for Michael's absence in family court.
Jones's gun is identified as the weapon that killed Michael's father, forcing Sipowicz and Clark to investigate him.
The brother of a mentally disabled man is found dead. A con artist rents the same apartment to several parties.
Sipowicz comes across Bale's credit card at a suspect’s house; a respected lawyer is shot in his car; Murphy and Ortiz investigate a drive-by shooting.
Sipowicz and Clark investigate the shooting of a former hooker who was kept by a married man. Ortiz and Murphy investigate a man with two wives and a murdered lover.
Sipowicz and Clark investigate a serial killer who infiltrates AA meetings and preys on female members by strangling them and smudging their lipstick as his trademark. Ortiz and Murphy go undercover in a sting operation to catch the AA killer. A man is found stabbed to death in his apartment, which is full of steroids.
Sipowicz and Clark investigate a restauranteur's murder and find that he had a prediliction for little girls. Ortiz is surprised to find that the Joint Narcotics Task Force has her cousin's boyfriend under investigation.
The remains of a business owner with ties to Columbia is discovered. A teenager from a wealthy family is found beaten to death in an area frequented by drug dealers.
When an elderly millionaire is found smothered to death, Sipowicz and Clark are called to investigate who had the motive, one of his staff or his trophy wife. Sipowicz prepares to be promoted to sergeant.
After an army sergeant is found murdered, Clark takes up the investigation and quickly suspects the brother of a soldier killed in Iraq.
The squadron gets frustrated when their temporary boss is more interested in his golf games than police work. Murphy and Ortiz investigate the murder of a young Muslim bride. Bale recommends that Sipowicz take over as squadron commander.
Sipowicz is forced to make tough decisions after the investigation of a prostitute's murder is linked to the police department.
Murphy and Clark investigate a fellow officers shooting. Clark also investigates the spousal abuse of a religious man towards his wife.