Sipowicz meets with a priest to talk about his troubles and finally sees the light. Afterwards, he, Simone, and Russell work together to investigate a robbery where an auto mechanic got shot to death. Following the apprehension of a wounded suspect, the detectives also arrest the suspect's younger brother who is unwilling to make a statement against his brother out of blind loyalty. Meanwhile, Medavoy works on finding a new place to live while he, Martinez and Lesniak work on finding the suspect of a drug-related double murder. John Irvin passes out farewell notices to the employees when he announces that he is moving back to the 1st Precinct uptown. Simone and Russell plan a trip to the beach. Medavoy meets Anne McGuire, a new detective, while working on his case. Elsewhere, Lucy is disruptive at work and Fancy tries to find a way to transfer her out of the building. Baby Theo gets baptized which seems to bring Sipowitz and Sylvia back together.

The detectives investigate the bombing of an abortion clinic that killed a guard. The squad gets a new lead on an old murder case. Ortiz's husband, Don, is murdered by his mistress' husband.

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.

The squad investigates two homicides: a gay man who hit his head after being punched out and another man shot on the street. Rodriguez is set-up by iab to take a bribe from an old friend.

The day's cases include an armored car robbery that left one guard dead, and the homicide of a woman whose body was found in a garbage truck; Sipowicz intervenes in the iab's case against Rodriguez.

A bomb threat is received at the courthouse. John Clark is placed on restricted duties pending charges for murder of the prostitute. John Irvin buys a new car only to be carjacked on the first drive.

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.

The detectives investigate the murder of a homosexual man who gave room and board to Latino parolees in exchange for sex; McDowell and Ortiz search for clues when a community activist is stabbed to death.

The detectives hunt for a man suspected of killing minorities to avenge injuries his brother suffered during the first Gulf War; Sipowicz and McDowell plan to marry.

The detectives investigate the shooting death of a man whose brother is a registered sex offender; and when Captain Fraker's trial gets underway, Sipowicz worries that his own testimony may have harmed the prosecution's case.

Sipowicz and Clark investigate the death of a transvestite whom a friend insists was having a relationship with a married man; a surgeon's hand is badly cut during a robbery; and Rodriguez testifies in the Fraker trial.

The detectives search for clues when a group of perpetrators torture a man for no apparent reason; a woman reports her husband as missing, but Sipowicz and Clark suspect she's not being completely forthcoming; and Fraker testifies in court.

The detectives investigate the strangulation death of a former porn star; a thirteen-year-old boy holds the key in implicating his father in his mother's murder; and the jury reaches a verdict in the Captain Fraker trial.

When a convicted rapist is found shot to death, his victims become suspects in the murder investigation; and Sipowicz searches for answers when a stranger targets Theo as he walks home from school.