Janice's murder trial begins, where Kelly risks the consequences when he testifies on Janice's behalf about their brief affair which results in the Internal Affairs Bureau investigating him. Meanwhile, Sipowicz works with an abused woman who's reluctant to testify against her husband. Medavoy, Martinez, Sipowicz and Kelly investigate robberies of drug dealers in their apartments. Sipowicz's AA sponsor wants him to agree to abide by a contract before he lets him try to restart his relationship with Sylvia. Donna tries to give Medavoy advice about dealing with his divorce. Also, Robin leaves Kelly for good when he tells her that he still has feelings for Janice.

Internal Affairs begins to investigate Kelly and Sipowicz's arresting of the officers they caught robbing drug dealer's apartments, then they begin looking into Kelly's handling of the notebook that was part of Medavoy's case. Janice's murder trial continues where she takes the witness stand to give an emotional testimony about her reluctant involvement with the mob and is sent to prison with a two-year sentence. Meanwhile, Kelly and Sipowicz investigate a double murder.

Martinez investigates a baby that was killed in a car from an apparent drive-by shooting. Meanwhile, Lois Snyder contacts Sipowicz for help because a policeman that she was entertaining died in a compromising position and he moves the body to a less conspicuous location. Lesniak's ex-boyfriend, Officer Abruzzo, keeps showing up at the precinct and harassing her, while at the same time, Lesniak locks horns with the officious Vince Gotelli over his working skills and his racy items he keeps. Kelly's future with the department is decided when Internal Affairs comes to the precinct to re-investigate some of his old cases and the result is Haverill transferring Kelly to borough dispatch duty. But Kelly decides to quit the force and after saying goodbye to Sipowitz, he throws in his badge for good.

Sipowicz investigates the murder of a pimp in which evidence points to a cop that Sipowicz once helped out with a problem of his. Later, Simone mentions the case to his girlfriend reporter Benita, and soon regrets it when the story hits the papers which leads to the suspect committing suicide. Benita denies leaking the story, but Simone refuses to believe her and ends their romance. Meanwhile, Donna's former boyfriend, Harold, a ex-New York Ranger hockey player, returns to the city and meets with Donna, while Meadvoy overreacts with jealousy. Donna confides her situation with her sister, Dana, but she manipulates Donna by sowing seeds of anxiety into her about Medavoy and his neurosis. Elsewhere, Martinez begins to develop feelings for Lesniak.

Fancy is less than enthused when Ronnie Drucker, a detective under surveillance by Internal Affairs, is assigned to the squad and Simone is asked to keep an eye on him. Both Drucker and Simone work on a case where an elderly man has been accused of exposing himself to a young boy. Sipowicz, Martinez, and Russell investigate the murder of a pimp in a laundromat which is witnessed by a young homeless woman who turns out to be Holly, the teenage runaway who helped the detectives out on a previous case (from 'The Bank Dick' episode). Meanwhile, John Irvin asks Sipowicz if he should approach Lesniak to congratulate her on "coming out." But she won't listen to his gay pride talk as does everyone else.

Simone and the men from Internal Affairs share the suspect after Simone gets some information from his incarcerated friend, Ray, about a case that Mike Roberts once worked on. Meanwhile, Fancy and Sipowicz both work on the case of a self-confessed gunman in a neighborhood shooting, once they get the story they help the shooter out. Medavoy investigates the assault case of an actor who was injured in a staged fight that went awry.

Simone and Sipowicz investigate a murder, but the procedures they must follow make them unpopular at the precinct when a fellow cop might have been involved. Meanwhile, Medavoy and Kirkendall investigate the murder of a young girl where the only clue is a videotape that starred her crushing worms. Russell goes missing and eventually turns up in Simone's apartment where she recalls to him that her father molested her as a child.

Simone and Sipowicz get another case involving the shooting of a rap artist who refuses to cooperate with them in the identification of his assailant. Meanwhile, Abby tells Medavoy that she and Kathy are trying to start a family and asks him to donate his sperm to her so Abby will get pregnant. Officer Szymanski, the racist cop who pulled over Fancy, tells him that he thinks Fancy was one of the ones responsible for his being set-up and caught in the alleged theft of a drug dealer's money. Also, Simone is approached and propositioned by FBI agents to help them with their ongoing investigation into the affairs of mobster Joey Salvo. Elsewhere, the night shift detective, Vince Gotelli, tells Simone and Sipowicz about a heart medical condition of his.

An inebriated Vince Gotelli is arrested after "hijacking" a city bus and having it wrecked. Fancy meets with the bus driver's boss to work out an arrangement about their investigation and suggests that Gotelli take some medical treatment. But it takes a forced intervention by Martinez, Medavoy, and Russell to convince Gotelli to get medical and psychiatric help in which Gotelli decides to throw in his badge for good. Meanwhile, Simone's continuing help with the FBI makes his life miserable when the men from Internal Affairs investigate him for the government license plate number on Salvo's car that he ran and is frustrated when he cannot tell them, not even Sipowicz, about what he's doing. Elsewhere, Sipowicz and Simone investigate the beating and murder of a woman in her apartment and deal with the emotionally sensate superintendent of the building whom they think he knows more than he's telling them.

Simone's continued involvement with the FBI sting against Joey Salvo jeopardizes his career when the men from Internal Affairs investigate him and suspend him from active duty. Meanwhile, Sipowicz and Russell investigate the gruesome murder of a young woman where a psychiatrist, named Dr. Wentzel, insists on implicating his patient's father for her murder. Martinez and Medavoy have a hard time over a haughty mugging victim who is a writer from a local magazine that wrote a bad story on the cops of New York City. Simone's involvement with the FBI reaches a cliff-hanging climax when in a secret meeting with Salvo, the mobster is hit by gunfire by an unseen assassin. Sipowitz, following Simone, comes on the scene and sees Simone standing over Salvo's dead body... and thinks Simone killed him!

In the four months since Joey Salvo's assassination, Simone is working odd jobs since he has been suspended by Internal Affairs pending their investigation, while he approaches Sipowicz asking about his and others incitements by the FBI who think that Salvo's death was an inside job within IAB, and Lt. Shannon from IAB tells Lt. Fancy that he may know the person who killed Salvo. Meanwhile, Gina discovers herself to be pregnant, but is hesitant on telling Martinez.

Medavoy launches his own investigation when Abby, and her girlfriend Kathy, are both shot by an intruder in their apartment in which Kathy dies and a grief-stricken Abby cannot bring herself to answer Medavoy's questions about her past and her former lover who may have been the assailant. Meanwhile, Simone, Sipowicz and Russell investigate a suspect after the charred body of a young woman is found in an abandoned vehicle. Also, Gina develops complications with her pregnancy and is taken off work for a few weeks.

The detectives search for the truth when a white off-duty police officer with a history of racism fires upon an African-American undercover cop. Dolores is arrested for shoplifting.

The detectives find themselves caught between the F.B.I. and Internal Affairs when an off- duty officer is killed during a robbery. Medavoy falls victim to Sipowicz's mischievous prank.

A shooter fires upon Fancy during a stakeout. Sipowicz fears that Dornan's demotion may be linked to the reopening of the Suarez case.

Sorenson and Sipowicz investigate when a fellow officer shoots a drug dealer; Russell and Kirkendall intercede on Gotelli's behalf when a disgruntled man repeatedly vandalizes his mobster neighbor's car.

Danny and Andy catch an assault that looks like it was done by the boys in blue. Jill considers dating her ex-husband.

IAB is closing in on Jill. Jill explains the leverage Don has over her. Andy stays by Theo's side as he undergoes tests to determine if he has cancer. Changes are made in the department as fallout over Jill's ex-husband.

The detectives investigate a multiple homicide at a fast food restaurant; an addict gives his 5 & a half year-old daughter to a drug dealer as collateral on an overdue loan; Internal Affairs reopens the Kirkendall case.

Andy witnesses a hold-up in the street and shoots at the get-away car. Det. McDowell is assigned to fill in at the squad again.

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.

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.

IAB start interviewing the officers who were in the diary, and Sipowicz and Clark are blamed as rats. A social worker appears to have taken her own life. A former cop wants his ashes buried at the precinct.

Andy and Theo move out. Tony thinks about calling it a day with his ex-wife. Sipowicz and Clark Jr look into the threats made to Clark Sr. A distressed, schizophrenic young man keeps saying "she can't breathe".

In hopes of freeing Clark from jail, Sipowicz searches for drug dealers who might have a connection to Laughlin; McDowell and Ortiz investigate a series of rapes in a park involving a perpetrator who forced his victims' boyfriends to watch.

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.

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.

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.

After being shot outside a bar, Sipowicz discovers the identity of the person who's been harassing him.