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.

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.

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.

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.

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.

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 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.

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.

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.

A foreign prince and princess are assaulted - the princess goes into a coma. Sipowicz and Simone investigate, with Mike Roberts help, who provides them with some information about Prince Foresmann's contacts over some stolen artwork. Meanwhile, Martinez's first delegate situation gets a resolution that keeps Officer Ortiz out of trouble with the department. This doesn't work out as planned when two women claiming to be his wife are arrested in a scuffle. Russell begins a new undercover job that involves her getting into a relationship with alleged drug dealer, Jimmy Liery, that might require her to start drinking again. Elsewhere, Geri continues to try to win Sipowicz's affections and Medavoy for once feels good about himself after his diet. Also, Martinez asks the anti-crime PAA, Gina Colon, out on a date.

Sipowicz and Simone investigate the murder of a woman whose body was found dumped in an alley and information about the mystery woman reveals that the woman was a mail-order bride from Russia who was looking to divorce her husband. Meanwhile, Medavoy and Martinez look into the drive-by shooting on a city bus. When one of the passengers mouths off his hatred of gays, both Medavoy and Abby become angry in which Medavoy slides on a further decline when he breaks his diet and begins to show off aggressive methods against the smart-mouthed gang members they bring in for interrogation. Elsewhere, Sipowicz starts working a part-time job for the U.S. Marshall by doing garbage detail at J.F.K. airport.

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!

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.

Simone and Sipowicz investigate the murder of two roommates. Meanwhile, Medavoy investigates a story from an old friend about a man wanting to hire a hit man for a job, and he recruits Martinez for the part of playing the hit man so they can catch the crime in the act. Kirkendall and Russell investigate the claim of a wealthy woman that her maid did not accidentally donate the diamond that the woman kept in a safe place disguised as a soup can.

Simone and Sipowicz investigate the murder of a nurse where the suspects include a struggling actor, a crazy man, and eventually a uniformed officer from the precinct named Tommy Richardson. Meanwhile, Medavoy and Kirkendall look into the death of a bicycle messenger who was killed for just trying to help a man whose backpack was stolen, so they determine that the backpack contained drugs. When they get a suspect into custody, Kirkendall figures out a clever way to get an ID on the suspect who won't cooperate. Also, Sipowicz's doctor tries to talk to him about how to deal with his medical problem, but Sipowicz won't listen.

Simone and Sipowicz work with Cohen to investigate the death of one of Cohen's witnesses and her son. Evidence points to the opposing attorney having some involvement with the arrangement of the homicide. Meanwhile, Russell and Kirkendall try to help a man locate his missing daughter. Medavoy and Martinez look into a corporation dealing with fake sports memorabilia, where Medavoy is taken in with the blond employees who reminds him of the departed Donna. Also, when Sipowicz thinks about his low sexual functions, his doctor prescribes the wonder drug Viagra. In the mist of all the cases, Simone and Russell decide to get married on their lunch break, but their cases get in the way of it all.

The detectives investigate a grisly murder in which an elderly woman's hands and feet were cut off. Simone's health continues to deteriorate.

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.

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.

Andy is finding Theo a challenge. A man is found dead in a hotel bath-tub, minus a part of his anatomy and some personal effects. A mother brings her son into the house because she thinks he's been stealing.

Fancy tries to rebuild his relationship with Abner; Andy and Danny investigate the murder of a club owner; Jones takes out his frustration on a man who is suspected of raping and beating a woman.

A female officer is shot following a stationery store robbery and later dies in hospital. Danny tries to keep Diane safe. A new ADA arrives. Katie decides to move back home.

Danny could be in big trouble for roughing up a suspect. Detective Connie McDowell joins the team for the day.

Sipowicz is hailed a hero after killing the man responsible for Sorenson's murder. While Lieutenant Rodriguez teams up with another precinct to investigate the robbery of his mother, the squad investigates the murder of two men affiliated with NYU.

When Clark's badge is stolen, the squad scrambles to find the thief before Clark must report the loss, which could ruin his career. McDowell and Gibson investigate a murder involving a young pregnant girl.

Sipowicz, Clark, Medavoy and Jones investigate a double homicide at a Latino restaurant. McDowell and Ortiz contend with a possibly mentally unstable woman who's posing as a cop.

The detectives investigate two crimes: the murder of a back-alley cosmetic surgeon and a violent rape; Clark finally takes Laughlin on in the boxing ring.

Maya's partner in anti-crime is killed. A little girl is snatched off the street. Connie becomes foster-mother to her niece.

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.

Sipowicz and Clark investigate when Julian Pisano is wounded in a shooting incident; McDowell and Ortiz assist a woman who doggedly pursues justice when she's conned out of $100; Clark grows concerned when his father stops returning his phone calls.

Sipowicz and Clark search for an African-American driver who fled the scene of a hit-and-run accident after unwittingly running over an Italian mobster's young daughter.

Andy and John approach Mrs Clifton for help with her daughter's murder. Jennifer turns up out of the blue, apparently off her meds. A man is shot, apparently over a church and a video tape.

The detectives search for a suspect who killed a businessman by blowing up his car; and Ortiz and Murphy investigate the beating death of a student.