Season 2

Licalsi tries to plea bargain his case and only get six years in prison for the murder, but Kelly is greatly opposed to the bargain after realizing he's in love with Janice. After learning that Kelly still has feelings for Janice, Robin ends their relationship. Meanwhile, Sipowicz and Kelly go on a stakeout of an apartment complex that have been the target of several robberies.

Licalsi takes the stand during her trial. The Internal Affairs Bureau investigates Kelly and Sipowicz in regards to the arrest of Officer Guyce and Officer Quint. Meanwhile, Kelly, Sipowicz, Medavoy and Martinez investigate the murder of a black couple.

Kelly investigates the death of an undercover cop in Chinatown, and to do so he must accept help from a prominent Chinese gang leader. Meanwhile, Sipowicz finds out that a former abuse case he had worked on has escalated into homicide; and Medavoy and Donna's relationship is revealed after Lt. Fancy catches them in the act, leading to Fancy warning the precinct against interoffice relationships.

Kelly's future with the force is decided as he investigates the death of an 18-month old baby shot in a drive-by while riding in a car driven by Duane Rollins. Though everyone believes the act was random, Kelly believes that Rollins was the intended target. Meanwhile, Sipowicz finds the body of a cop, and must continue dealing with both his commitments to Alcoholics Anonymous and his feelings for Sylvia Costas.

In Kelly's absence, Detective Bobby Simone joins the force and is assigned to work with Sipowicz on a case involving the murder of a mob member's son. Later at the precinct, her boyfriend, Detective Jimmy Abruzzo, threatens Detective Lesniak with a gun; and a woman claims her husband is sexually abusing her 14-year old daughter.

A chiropractor's wife is found murdered and Simone and Sipowicz discover that the chiropractor, Dr. Peter Shennon, was having an affair with his secretary, Judith Krasky, which turns all suspicions towards him. Meanwhile, while working for a security company, Martinez falls for Leticia Beltran, a college student he's assigned to protect. Later, a woman, Christine Williamson, brings Simone a gun she found her 11-year old son playing with.

An 11-year old boy admits to killing an Hispanic student in the midst of a turf-war at his elementary school, but Simone has a suspicion that the boy is taking the fall for someone. When a ladies' man, Eddie Reyna, learns he's HIV positive, he becomes targeted by one of his former lovers that he infected with the disease. Meanwhile, Donna's sister, Dana, comes to town for a visit, which causes a rift between Donna and Medavoy.

Sipowicz and Simone are assigned to the case of a pregnant woman who was murdered and the only charred remnants remain, which means there are few clues for the detectives to go by. Meanwhile, Sipowicz grows increasingly concerned when a close friend, Dan Breen, is badly beaten by his mentally handicapped son, Danny.

Simone and Sipowicz investigate the murder of a gay bar proprietor and have transsexual Candace La Rue as a material witness. Dan Breen decides to visit his mentally disturbed son, Danny, despite Sipowicz warning him not to do so. Elsewhere, Medavoy investigates a fortune telling scam after a woman is conned out of her life savings; and Lt. Fancy's wife goes into labor.

Detective Soloman tries to use his status to steal a case from Detective Simone after Simone arrested a notorious serial killer, Putnam. Meanwhile, Commander Haverill tricks Lt. Fancy into lying about a case involving a crime lord; Lesniak goes after a flasher; Sipowicz once again proposes to Sylvia Costas; and Benita Alden, a reporter, flirts with Simone.

Simone and Sipowicz follow hot on the trail of the "Webster Dictionary" serial killer, though bureau politics take their toll on the case. Meanwhile, Sipowicz uses Vinnie Greco as an informant in order to try to stop a bank heist; and Lt. Fancy enlists Greco's help in order to get even with Commander Haverill.

The detectives investigate the brutal murder of a young woman. Their investigation leads to one main suspect – Derrick Cobb, the girl's former stepfather. Simone worries that one of his close friends, Raymond diSalvo, has gotten involved in drug dealing at a dance club. Lesniak investigates con artist Mac McClellan.

Three fast-food employees are murdered execution-style. As Simone and Sipowicz investigate the murders, Martinez and Lesniak look into the attempted rape of an elderly woman. Meanwhile, Sipowicz and Sylvia Costas have differences when it comes to planning their wedding; and Martinez becomes jealous when Lesniak has lunch with an old friend, Dr. Druzinski.

Simone and Sipowicz investigate the death of a pimp, but all evidence they find points to one of their own, Jerry McCabe. Medavoy's constant jealously causes Donna to rethink their relationship and Simone begins to worry that Benita Alden is using him for her career gains.

Simone and Sipowicz are assigned to investigate Vartan Illiescu, an immigrant suspected of being a terrorist. An unknown person kills George Putnam, a serial killer, out of revenge before he can be tried in court. Meanwhile, Medavoy and Donna's relationship crumbles after Medavoy gets advice from Dana.

Simone and Sipowicz are put on the case of a teenager known for his graffiti work who was brutally murdered. Meanwhile, Donna continues to contemplate her relationship Medavoy; and Sylvia is mugged, which results in a deep secret being revealed to Sipowicz.

Simone has to convince Joyce Novak, a witness in a double-homicide case, to testify. Sipowicz is assigned to investigate the murder of an elderly woman who was the owner of a candy store he worked at when he was growing up.

A man goes on a shooting spree, killing a waitress, two cops and three other citizens before he was apprehended. Meanwhile, Lt. Fancy speaks on behalf of Reggie after Reggie squares off with Sgt. MacNamara.

Simone becomes attracted to an undercover cop, Diane Russell, as they work together to capture an arsonist. Sipowicz becomes personally involved in a case after a woman he convinced to testify in a case is murdered. Martinez and Lt. Fancy square off at the annual department boxing tournament.

Help comes from an unexpected place as Sipowicz and Simone investigate the murder of a bookie. Joyce Novak, a witness to a murder, charges Simone with sexual harassment. Meanwhile, Sylvia and Sipowicz head to religious counseling to prepare for their upcoming nuptials.

An ill infant becomes the missing link in a serial rapist case Simone and Sipowicz are investigating. Simone suspects Russell of trying to cover up a serious problem; Medavoy considers getting back together with his wife with whom he is separated; and Irvin asks Simone for help when police officers assault him and his lover.

Sipowicz tries to get a confession and capitalizes on a mistaken identity. Lt. Fancy's brother is falsely accused of accepting bribes and Simone is able to uncover the truth behind the crime. Russell's apparent hangover almost results in a hazardous situation during a sweep. Later, the precinct throws a bachelor party for Sipowicz, who is noticeably dealing with pre-marriage jitters.