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.

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.

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 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.

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.

Martinez is shot in the back during a scuffle and the doctor's report is possible that he may be paralyzed for life. But Martinez's assailant, a government witness in a relocation program, will probably go free and Simone contacts reporter Benita Alden, his former girlfriend, to help put pressure on the D.A. to prosecute their protected witness. Meanwhile, Russell, on the road to recovery from her alcoholism, wants Sipowicz to let Simone know she's doing okay but she is on the brink of falling off the wagon. Donna expresses to Simone that she has feelings for him, and Sylvia tells Sipowicz that she may be pregnant.

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.

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.

An Indian woman is found dead in a car and Sipowicz is full of theories about who killed her and why. While Donna is away at a computer camp taking courses for the week, her temp is a feisty middle-aged woman, named Evelyn, who has bad attitude and who clashes with Sipowicz and others in the squad as well. Meanwhile, Martinez and Medavoy are nearby when a drug crazed man, named Marv, tries to rob a couple of stores of credit card slips. Russell and Lesniak work on another case involving a man who was left to die of a drug overdose that leads to a chance of mending the feud between them.

Sipowicz becomes annoyed when federal agents take over their investigation of the disappearance of a millionaire. Then a petty criminal from the past surfaces with information about the kidnapping and Sipowicz decides to act on it. Meanwhile, Simone aids an old boxer friend of his, who happened to got him started with bird breeding.

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.

Medavoy and his wife, Marie, split up once again and she comes down to the station to have some hard words with Donna, while he decides to crash there since he cannot afford a place to live. Meanwhile, Simone and Sipowicz team up with Detective Harold Ng to probe the death of a Chinese girl whose leg has a strange marking on it which may have been self inflicted. Martinez and Lesniak look into the robbery case where a woman in a wheelchair lets a man claiming to be a policeman into her apartment, while the husband reveals a clue to Martinez that he has been seeing a prostitute on a regular basis and whose pimp might have planned the robbery. Elsewhere, Sipowicz does not want to accompany Sylvia to her latest doctor's visit, and Martinez gets an opportunity to find out where Lesniak really stands on her sexuality if she's really gay.

Sipowicz has race relation problems with the organizer of a local basketball game, held in the memory of a young boy, which erupted into violence by the gang members on the opposing sides which left two dead and seven wounded, and was witnessed by a reporter. Fancy has problems when Sipowicz racist colors come to light and has him removed from the case, much to his anger.

Simone and Sipowicz look into the death of a young woman whose body is found burned beyond recognition, except for a tattoo on her back. Detective Vince Gotelli arrives from another precinct to assist Simone and Sipowicz with their case and puts his two cents in, much to Sipowicz's delight and one of the victim's roommates becomes the prime suspect. Meanwhile, Medavoy pulls double shifts for himself (to get away from problems at home) and is assigned to watch an informant who has a penchant for playing poker with his friends.

A strange woman walks into the precinct and gives Sipowicz and Medavoy some information about a disappearance that occurred eight years ago and where the body may be located. Meanwhile, domestic violence in Russell's parents apartment leads to tragedy when her drunken father is found murdered in their apartment and her brother, Doug, claims to have shot him in self defense. But Simone thinks otherwise and presses to get the truth about what really happened to her Russell's father and soon learns that Russell's simpleton mother in fact did the deed and Doug is trying to take the rap out of blind loyalty to the family.

Russell worries about her mother's pending grand jury trial for the intentional murder of her father. Meanwhile, Sipowicz and Simone search for the killer of a mobster's son, that reveals a family affair. The pompous lawyer of a suspect in another murder case impedes Medavoy and Russell's investigation and the erratic behavior of son of the victim doesn't help much either. Also, Martinez and Lesniak investigate another murder case that may be connected to Sipowicz and Simone's murder suspect who now may be on a killing rampage.

Donna and Simone give Lesniak and Martinez advice, respectively, on their plans for their first date and night together. Afterward, Simone and Sipowicz investigate the death of a young woman who was brutally murdered in her apartment and Simone and Martinez travel to Atlantic City to apprehend their suspect. Meanwhile, Medavoy and Russell try to find the perps who shot a wealthy and shallow surgeon during a mugging, and they also deal with surgeon's petulant wife who wants to press charges against her husband's mistress when she learns that she was in his company during the robbery.

Simone and Sipowicz get another murder case where a mild mannered professor is found decapitated in his apartment. Meanwhile, Martinez is helping out a former porno actress who is getting harassing phone calls, but Lesniak is not comfortable with the situation. Andy Jr. arrives in town with some news for Sipowicz, but he can't find the time to tell his father and finally at dinner, he explains that he has just been discharged from the Air Force and is joining the police department in Hackensack, New Jersey.

A detective from another precinct, Martina Escobar, joins Simone and Sipowicz with their investigation of a rapist/murderer who is throwing small children from the tops of buildings. Meanwhile, Martinez and Russell investigate an alleged case of date rape, but the women of the squad and Sylvia have a major disagreement with Martinez's decisions regarding the suspect. Elsewhere, Sipowicz shows his son the ropes of being a cop.

Simone makes contact with Ferdinand Hollie, an old informant, who wants to help him capture a pair of Colombian drug dealers who killed a young girl with their crossfire. But Hollie, a drug addict who is HIV-positive, has his own agenda to rob the Colombians. Meanwhile, Russell is paired with Sgt. Ray Kahlins, a "blowhard" from the federal anti-drug unit who is more interested in collecting overtime pay than catching a separate pair of drug dealers during a stake out. But Kahlins' brash tactics and disrespect for Simone and his informant Hollie, put both cases at risk. Also, Medavoy and Martinez investigate the murder of a Santería priest found in a local sewer and try to link a parole officer and a recent parolee to the crime.

Simone and Sipowicz help a local FBI agent, named Mike Frances, to investigate the murder of a local Italian mobster. However they are forced to commit robbery while working undercover for Agent Francis, and have to place a bug in the mob hangout. When two wise guys come to the station to file a robbery complaint, Russell and Medavoy catch them in the act of filing a false report. Meanwhile, Donna's hairdresser, Marina, tells her that she has a problem with her ex-boyfriend. He wants to hijack Marina's current boyfriend's truck, and Martinez goes undercover as Marina's boyfriend. But Lesniak is unable to hide her jealousy and possessiveness. Elsewhere, Andy Jr. learns more about being a beat cop with more pointers from his father Sipowicz Sr.

Sylvia is now nine months pregnant and ready to give birth any day so Sipowicz is on the edge. Meanwhile, Simone and Sipowicz, with Andy Jr. along for the ride, investigate a case where the drug-addicted nephew of the victim of a robbery-homicide is found holding the stolen goods. Meanwhile, Medavoy, Martinez, Lesniak, and Russell all join forces to work on the robbery-murder of a bouncer where the leads first lead to a biker, then to a check cashing forger, and to his co-worker. In the mist of the investigation, Martinez and Lesniak finally reach an agreement that they are not right for each other and quietly break up by agreeing to try a platonic relationship. Also, Donna contemplates an administrative job offer in California.

Just days after Sylvia gives birth to a baby boy (Theo), Sipowicz suffers an emotional setback when Andy Jr. is found murdered in the line of duty. Sipowicz wants Simone to lead the case of his son's killer and also wants the opportunity for restitution. With Russell in tow, Simone tries to balance his desire for revenge, as well as his quest for justice to catch the killers. While Sipowicz breaks the news of his son's death to his first wife, Katie, he begins to show signs of an emotional breakdown. In the midst of all this turmoil, Donna makes her decision when she quits her job as administrative assistant to the precinct and moves to California, leaving New York for good.

Sylvia confronts Sipowicz about her suspicions that he is going to late-night bars and drinking again, and the effect is everywhere. Lt. Fancy is forced to sent him home after Sipowicz walks in one morning drunk. Sipowicz even fights with some street punks, gets beaten up, and Simone offers to look for the men that beat Sipowicz up. Meanwhile, a new administrative assistant, named Lucy, arrives as Donna's replacement. Also, Russell investigates a young woman, named Angela, who claims to have been stabbed by her jealous boyfriend. Simone, following a lead from a streetwalker named Deena, finally tracks down and confronts the two thugs who murdered Andy Jr. and guns them both down in a hail of bullets.

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.