A group of detectives and officers work at the 15th Precinct, a seedy police station in Manhattan, New York City. Detective John Kelly, a 15-year veteran of the force, deals with his partner Andy Sipowitz, an alcoholic 20-year veteran detective. Laura Michaels, an aspiring lawyer and Detective Kelly's wife, is having problems with their marriage and she hires Josh Goldstein, a lawyer who lives in apartment 4B of their building to work on a divorce, who gets mugged in the laundry room of the building. Meanwhile, Sipowicz is relentlessly pursuing mobster Alfonse Giardella, who threatens Sipowicz to leave him alone. Later, Sipowicz is shot by Giardella during a tryst with a prostitute. Enraged, Kelly orders the precinct officers to hound Giardella and his ruthless employer; mafia kingpin Angelo Marino. The new patrol officer, Janice Licalsi, is attracted to Detective Kelly. But is she is revealed to be an informant for Marino who orders her to murder Kelly.

Inspector Lastarza of the Organized Crime Unit tells Lt. Fancy and Kelly that they stop applying pressure to the local mob for their pursuit of Angelo Marino is hurting the FBI investigation to nail Marino. Meanwhile, Sipowicz regains consciousness in the hospital after the shooting, but he has no memory about the attempt on his life because he was drunk at the time. Laura and John Kelly become officially separated and she decides to join a private law firm. Josh "4B" Goldstein becomes more paranoid about his mugging and brings a gun into the laundry room every night in hopes to catch his attacker. Kelly tries to reason with a deranged man who has taken a judge hostage who let his son's killer free. Elsewhere, Angelo Marino puts more pressure on Janice to murder Kelly, but she kills him and his chauffeur/bodyguard instead and slips away.

Janice's policeman father arrives for a visit and tells her about his pending indictment for corruption involving being an informant for Angelo Marino when a book that Marino had on him as a list of all of his informants... including hers. Sipowicz makes some appearances at the hotel where Giardella is staying to further intimidate him over the shooting death of Marino. Meanwhile, Kelly and Martinez are assigned a case involving the robbery and murder of a woman. Also, Josh Goldstein comes to the precinct in search for his gun he used to kill his assailant.

Kelly begins moonlighting as a security guard for Susan Wagner, a wealthy woman who's married to an abusive husband. But things take a turn when the husband is shot and killed, and Mrs. Wagner becomes a suspect. Meanwhile, Sipowicz is paired with the hard-nosed Detective Walker who arrests a man for a robbery and double-murder. While Detective Walker thinks he's guilty, Sipowicz thinks differently. Laura quits her job and plans to move into a position with the District Attorney's office, prosecuting narcotics. The increasingly edgy Josh Goldstein has Kelly appear at a tenant's readiness group regarding crime, and he is later killed trying to save an elderly woman from a mugging on a subway platform.

Martinez goes to visit his drug-addicted brother, but finds the superintendent of his building, Hanlan, is a retired cop who is on the take and is forcing the tenants out, and Kelly sets out to prove that Hanlan is responsible for the death of two of the apartment's residents. Meanwhile, Laura's new job as an Assistant District Attorney takes a turn when she's assigned to a case that involves Giardella. Also, the squad deals with Detective Stillwell, a prankster whose jokes in the station house get out of hand.

A shady homeless man, named Lou, comes to the station thinking he's a werewolf and demands to be locked up into a cell before he kills someone when the night comes. However, things take a turn when Kelly investigates Lou when he may be a witness in the murder of a nine-year-old immigrant boy. Meanwhile, Sipowicz is visited by his long-estranged son, Andy Sipowicz, Jr. with his fiancée, Patty Constance, an older woman who Sipowicz discovers that she has been cheating on Andy Jr. Elsewhere, Giardella is killed in his hotel room by a Mafia button man dressed as a window washer before he can testify to a grand jury against his superiors and Laura finds herself the only witness to the murder.

Janice is contacted by Richie Catena, a mob button man and former associate of Marino. They want her to start doing favors for them again or they will expose her past activities with the late Marino. Janice agrees to co-operate with them without telling Kelly, but she tells Inspector Lastarza who tells her to go along with it. Meanwhile, Martinez is distraught when he learns that his brother has died from a drug overdose. But their father, Hector, wants to go out and kill the pusher who's responsible for his son's overdose. Also, Medavoy celebrates his 40th birthday and later musters enough courage to ask Donna out on a date to an ice skating rink.

As Christmas draws near, the zone commander, Haverill, starts to come down on Lt. Fancy about his work skills and Sipowicz later intervenes and threatens Haverill to lay off Fancy or he will reveal some incriminating evidence about him being a racist. Meanwhile, Kelly and Sipowicz investigate the kidnapping of a doctor's daughter. Janice must pass some more information to the mob about the station's moves and wonders how she will get out of this situation. Also, Martinez and Medavoy question a woman and her young son who claim to have been robbed by a man who picked them up while they were hitchhiking in North Carolina. But Martinez later discovers that the woman, Kathy, is not who she claims to be, which leads to a hostage situation, involving Donna, at the station. Sipowicz reluctantly plays Santa as the precinct's annual Christmas party, and Martinez receives his gift from Lt. Fancy when he is promoted to detective, while Medavoy panics when the station's pet cat eats the Christmas rabbit, and Kelly visits his Alzheimers-stricken mother who resides in a nursing home.

The mob hit man who killed Giardella and who Laura can identify, is trapped on the roof of the building with a hostage. Martinez works on his first detectives case, which involves a fake ATM machine taking peoples money. Meanwhile, Fancy and his wife prepare to face a court date when a foster child they've been caring for is ordered back into custody of the real mother who's just been released from a drug rehab program. Sipowicz and Kelly investigate a shooting of mobster Tommy Linardi, whom had taken over the late Angelo Marino's organization, in which turns up a notebook that Marino kept which has Janice's name in it. Janice asks Kelly for help who decides to steal the notebook to protect her from further investigation to Marino's murder, while Fancy again locks horns with Inspector Lastarza over the handling of the case.

Medavoy leaves his wife and finally tells Donna about his romantic feelings for her, which turn out to be mutual. Sharon LaSalle, a police academy classmate of Kelly's, joins the squad and shortly after, she and Sipowicz investigate the death of her husband, Danny, who was an ex-cop trying to stop a robbery during her first day at the 15th precinct. Kelly and Sipowicz relentlessly try to track down the two robbers responsible, while an an ambitious publicity-seeking reporter plots to take advantage of the case to further advance his own career. Meanwhile, an alcoholic woman keeps lodging complaints to Kelly against her abusive husband that she never follows through with.

Sipowicz has a cavity and decides to have it taken care of by his son's dentist. At the dental office, Sipowitz finds himself unsuccessfully trying to prevent the suicidal Dr. Fleishman from jumping off a 28th floor ledge. Meanwhile, Medavoy and Martinez work on a strangulation murder case that appears to be the work of a cross-dresser. LaSalle's first case for the squad involves a woman who was raped and she, Kelly, Sipowicz try to catch the most probable suspect. Janice joins the undercover squad and is partnered with the hot-tempered Roy Larson to assist with LaSalle's case, while Sipowicz suspects that Larson's short temper and odd behavior points to a drug problem. Also, Lois Snyder (the prostitute who set Sipowicz to be shot in the premiere episode) returns to try to apologize to him about the incident and also wants to renew their romance. But Sipowicz turns her down and goes back to start whatever relationship she has with D.A. Sylvia Costas.

Lt. Fancy insists to a reluctant Larson that he take a drug test and when it comes back positive of methamphetamine use, he is fired. One of Detective Mike Roberts' informants/girlfriends comes to the precinct and causes trouble for him, especially when she later turns up dead, and Roberts becomes a suspect. Although Roberts ends up being cleared, his reputation is ruined and he decides to quit the police force. Meanwhile, Sylvia has trouble getting through to Sipowicz to give their relationship another try. Also, Laura appeals to Kelly to help her re-examine a case she is prosecuting of the alleged murder of an abusive man by his wife, in which Martinez and Medavoy investigate one witness and discover some conflicting facts in the case.

Medavoy suffers a stress-related anxiety attack while working and doesn't want to tell his wife about his personal problems, which displeases Donna who wants him to work things with his wife. Meanwhile, Sipowicz looks into the robbery of a wheelchair-bound Vietnam veteran, who later takes his muggers hostage. Elsewhere, Detective Kelly starts moonlighting as a bodyguard for Robin Wirkus, the young girlfriend of Jimmy Wexler, an ailing wealthy friend of Kelly, and Kelly later stumbles into a complex blackmail plot by an extortionist, named Stan, who asks Robin for sexual favors. Also, Laura tells Kelly that she have moved on with her life and is dating someone.

Sipowicz suspects a private investigator of bilking a father for the past six months in a scheme to find the man's runaway daughter. Meanwhile, Kelly and Sharon LaSalle investigate the shooting death of a 13-year-old boy and try to apprehend the gang member responsible. But when the killer escapes from the precinct, and injures LaSall in doing so, Kelly and the other detectives must try to stop the murdered boy's father who plans to go after apprehends the killer himself. Also, LaSalle has a chance to move out of the precinct and into a more regular routine of detective work in which she takes the offer and leaves the 15th Precint for good.

Mike Roberts meets with Kelly in search of getting some bodyguard and/or P.I. work for himself after quitting the police force. Meanwhile, Laura feels someone is stalking her and gets Kelly to meet her new boyfriend, Dr. Schrager, who may be the stalker. Elsewhere, Sipowitz and Kelly deal with a woman whose boyfriend was a material witness and is afraid to identify the hit man because he's afraid the hit man's friends will kill her next. None of the detectives are too excited when Haverill sends them down to Times Square for uniform detail at a parade.

After Robin's husband dies, she gets angry when his will seems to stipulate that Kelly should resume his duties as her bodyguard. Meanwhile, Sipowicz must clear his own son of a drug pushing charge. While investigating a tip on the location of a dead woman, Medavoy, Martinez and Kelly find another body of a dead man in a garbage dump which leads to Kelly suspecting a hotel concierge and the hotelier of conspiring to murder the hotelier's husband.

Medavoy tells Donna that he's caught his wife being unfaithful yet again and decides to move out. But he crashes at the station since he cannot afford a place to live. So, Donna asks him to move in with her. Meanwhile, racial hostilities flare up in the community after Martinez shoots a belligerent black motorist who draws a gun on Medavoy, but the gun goes missing. Janice becomes more and more distressed by the recent events and after talking to Kelly's preacher friend, Father Downey, she confesses to Fancy that she was the one that killed Angelo Marino and his chauffeur. Also, Sipowicz tries to attend an open AA meeting with Sylvia's support.

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.

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.

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 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.

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.

Medavoy and Sipowicz go undercover as Hasidic Jews to recover a stolen Torah. Meanwhile, Simone gets a case where a father suspects his intellectually disabled son of killing his daughter. Detective Stuart Morrissey tactics with the suspect does not sit well with Lt. Fancy, despite the facts that the case match the one Simone are working on. Also, Sylvia visits a doctor who confirms that she's pregnant, and Lesniak keeps checking up on Martinez still in the hospital.

Meadavoy and Lesniak pair up to identify who's launched a series of vicious attacks on a man. Meanwhile, Simone tries to locate a possible suspect in a series of rapes. Russell tries to maintain her sobriety and it's strongly tested when her parents domestic problems get out of hand. Also, Martinez finally gets out of the hospital and returns to duty. But in a final surprising twist, Lesniak tells Martinez that she likes him as friend only... because she happens to be gay.

Lesniak's preference of her lesbianism quickly gets around the precinct, which gives her mixed reactions. Meanwhile, Sipowicz clashes with Simone throughout their investigation of the senseless murder of two kids, which is only the start of a really bad day which also includes Sipowicz dealing with Sylvia's morning sickness, and Simone dealing with Russell who falls off the wagon.

A woman comes into the station to report that there's a bullet hole in her wall. The gun is found in Jimmy Liery's apartment and Simone arrests Jimmy, but has to let him go as there isn't enough evidence to hold him. Simone finds out that Russell unsuccessfully attempted to scare Jimmy by firing a shot over his head. Simone decides to remove Jimmy unlawfully by setting him up to take a fall. Meanwhile, Sipowicz is still angry at Fancy who thinks he held up his promotion. Following a tip from a young runaway teenage boy, named Marco, Medavoy and Martinez investigate the murder of an apartment building tenant. Also, artist Walter Hoyt (from ep. UnAmerican Graffiti) returns and wants the detectives help to get his paintings returned from some mob guys that he is a witness against.