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.

Kelly works with a Chinese detective in the investigation of the murder of an off-duty cop in Chinatown. Lt. Fancy catches Donna and Madavoy in an embrace and warns both of them about relationships in the workplace. The abused woman Sipowicz helped out turns up dead and her husband is a suspect. Meanwhile, a tough new female detective, Adrianne Lesniak, transfers into the squad because of a relationship she had with an officer at her former precinct in the Bronx and begins to work with Sipowicz on his case.

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.

Bobby Simone, a widower and homing pigeon breeder, joins the squad as Kelly's replacement. Simone's first assignment is to help Sipowicz in the investigation of the hit on a mobster's son, where a stray bullet also hit an elderly woman in her apartment. Meanwhile, Lesniak tries to help a woman who's worried that her husband is molesting their daughter, and an over-the-edge Abruzzo pulls his gun and threatens Lesniak in the squad room for leaving him.

Simone and Sipowicz suspect a chiropractor of murdering his wife. A woman whom Simone knows finds her 11-year-old son in possession of a gun. Meanwhile, Medavoy tells Donna that he has changed to a high-fiber diet a part of yet another change in his life. While moonlighting as a security guard for Mike Roberts, Martinez becomes attracted to Leticia, a college student he's been assigned to protect and she's worried about her possessive father, a Colombian businessman who may have criminal connections.

Donna's younger sister, Dana, arrives and moves in with her and Medavoy, and tries to make the moves onto him. Simone doubts the confession of his friend's 11-year-old son, a murder suspect in a gang related shooting at a school. Meanwhile, an HIV-infected Lothario comes to the station and asks Lesniak and Martinez for help when he appears to be targeted by a woman he's apparently infected.

Sipowicz's AA sponsor, Danny Breen, is beaten up by his estranged son. Meanwhile, Simone and Sipowicz investigate the murder of a pregnant woman whose charred body leaves few clues. Martinez and Medavoy check out the story of a man who might have information about a pawn shop robbery.

Simone and Sipowicz investigate the murder of a gay bar owner during the Christmas holidays. Meanwhile, Fancy's wife goes into labor to have her baby. Breen breaks his promise to Sipowicz by checking up on his son and decides to go back to him, which turns out to be fatal when Breen's son kills him and Sipowicz has to arrest him.

Lesniak deals with a perpetrator and his "high priced lawyer and shrink" when he repeats the offense. Meanwhile, Detective Solomon uses a fast pull to take a possible serial killer case away from Simone after he brings in a possible suspect. One of Fancy's old contacts, Vinnie Greco, brings in a tip about a couple of guys looking for some heavy arms to do an armored car job and Sipowicz works with him, but Greco is working for someone else against Fancy. Sipowicz invites Andy Jr. over at his place for dinner where his son tells him that he is joining the Air Force. Also, Sipowicz proposes marriage to Sylvia and this time, she accepts.

After discovering a key piece of evidence, Simone gets his chance by Detective Archie Solomon to question the serial killer suspect George Putnam. Meanwhile, Sipowicz, Medavoy and others work on how to stop the armored car robbery and Fancy has a confrontation with Haverill about using his informant, Vinny, as a pawn to try to bring him down and plays a tape for Haverill which he reveals his true attitude which results in his resignation as the zone commander. Also, Martinez and Lesniak arrest an odd extortionist, while romantic feelings for each other begin to appear, and Simone also develops romantic feelings for his writer friend Benita Alden.

Simone and Sipowicz investigate the brutal murder of the teenage daughter of a woman whose ex-husband has made threats against her. Meanwhile, Lesniak and Martinez's latest case involves them trying to nab a con artist who sells a black box to homely women, promising them beautiful skin. The new zone commander, Captain Clifford Bass, checks in and lets Fancy know his overtime policy, which doesn't sit well with Sipowicz when it compounds their investigation. Elsewhere, while Simone's romance with Benita becomes more serious, he also deals with a childhood friend, named Ray, who is now involved with a nightclub that is frequented by wise guys and other criminals.

Sipowicz disagrees with Sylvia over their wedding arrangements, for he wants to travel to Maryland for a quick one, whereas Sylvia wants a traditional Greek Orthodox service. Shortly thereafter, Simone and Sipowicz investigate an execution-style murder of three people at a fast food restaurant and the investigation leads them to travel upstate to look for a possible suspect. While there, Simone tests his homing pigeons by releasing them, hoping they will make it back to New York. Meanwhile, Lesniak meets an old high school boyfriend of hers, now a doctor, while investigating a rape case with Martinez, who develops a case of jealousy.

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.

Simone and Sipowicz collide in their squad car with a Romanian immigrant who has a woman locked in the trunk of his car and later, their investigation shows him to be a possible terrorist and holding a wealthy family prisoner with pipe bombs. Meanwhile, the serial killer, George Putnam is shot by an unknown sniper. Simone begins to investigate the father of the killer's last victim, Mr. Rudman, and another member of a victim's support group... who all appear to be part of a secret vigilante group. Medavoy talks to Dana about his relationship with Donna if he's losing interest in her, but the crafty Dana takes advantage of the situation to try to break them up by playing on his mental neurosis as the cause of Donna's lack of trust in Medavoy. Also, Martinez keeps asking Lesniak to go out on a date with him.

Simone and Sipowicz investigate the race-related murder of a Puerto Rican teenager who was attacked while spray painting graffiti in Little Italy. Meanwhile, Medavoy meets Donna's former boyfriend, Harold, when he comes to the station to file a car vandalism report, while Donna makes a tough decision about her relationship with Medavoy. Also, Sylvia is mugged and she later tells Sipowicz a secret from her past about being raped as a teen.

Simone deals with an emotionally fragile woman, named Joyce Novak, whom is a witness for a double-murder when she keeps changing her story, for she is really only interested in flirting with him. Meanwhile, Sipowicz participates in the investigation where a family-run business, that he used to work in, is held up and the owner's wife is killed. After Donna leaves town for a long vacation (and to get away from the annoying Medavoy), her temporary replacement, John Irvin, is a flamboyantly gay man whom Simone used to know from his old precinct. But Irvin makes the whole the station, including the bigoted Sipowitz, uncomfortable. Also, Martinez enters in a police department boxing tournament.

Simone and Sipowicz search for a killer following a shooting spree, which left several people dead and where a rookie cop's missed shot also killed a bystander. Meanwhile, Fancy's younger brother, Reginald, a policeman in the 8th precinct, has racial troubles with his commanding officer and Fancy intercedes on his behalf and his own boss, Captain Bass, covers for him. Sipowicz sees a doctor and discovers he has an enlarged prostate and Sylvia mistakenly thinks their lack of sexual activity over the past few weeks was because of the rape incident from her past that she told him about.

Fancy works with Martinez to help him get ready for the inter-precinct boxing tournament. Meanwhile, Simone is attracted to the new undercover cop, Diane Russell, who is working with him to catch a wanted arsonist in a sting in which Lt. Fancy's informant, Vinny Greco, returns to offer more advice and annoyance to everyone. Elsewhere, a woman that Sipowicz gets to testify in a case is murdered by the men she was going to testify against, and Sipowicz tries to prevent the murdered woman's husband from going after the gang members responsible.

Simone and Sipowicz search for a killer of a bookie in which Mike Roberts returns to offer his help. Meanwhile, Donna returns from her long vacation trip to resume her position at the station and her temp, John Irvin, gives everyone farewell greeting cards when he is moved to the anti-crime lab upstairs. But Donna continues to treat Medavoy with resentment which leads to him thinking that she might be finished with him. Simone's obsessive witness, Joyce Novak, goes too far when Simone rejects her advances after he tells her that she will not testify in the upcoming trial. This leads to Joyce attempting to murder Diane Russell when she correctly assumes that she and Simone are romantically involved. Sipowicz and Sylvia meet with the priest to help with their wedding and later she hears a story about what has contributed to Sipowicz's loss of faith.

A witness to a crime smells alcohol on Russell's breath and uses it against her, and Sipowicz smells the same. Simone then confronts Russell about her drinking, but she tells him to mind his own business. John Irwin comes to Fancy for help when he and his gay lover are beaten up by gay-bashing officers in another precinct. Meanwhile, a terminally ill infant helps the detectives locate a serial rapist. Medavoy meets with his ex-wife who tells him that they should get back together for their kids and when Donna finds out, she tells him that their relationship is over.

Pre-wedding jitters put Sipowicz in a rare form of panic whereas Sylvia remains perfectly calm. While investigating a murder in Chinatown, Russell's drinking problem makes her miss getting a gun off a suspect and she finally admits to Simone about her alcoholism. Meanwhile, Fancy's brother, Reginald, is still having problems with his racist sergeant and his belligerent attitude has resulted in him being investigated by Internal Affairs. So Fancy, Simone, and the squad work together to help clear Reginald of any misconduct. Martinez finally goes out on a date with Lesniak and asks her to be his date for the wedding. At the ceremony, Simone is Sipowicz's best man, Sylvia's father escorts her down the aisle and even Andy Jr. makes it just in time for the ceremony. Medavoy brings his ex-wife to the wedding while a lonely and jealous Donna painfully watches from afar.