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.

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.

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.

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.

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 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.

An inebriated Vince Gotelli is arrested after "hijacking" a city bus and having it wrecked. Fancy meets with the bus driver's boss to work out an arrangement about their investigation and suggests that Gotelli take some medical treatment. But it takes a forced intervention by Martinez, Medavoy, and Russell to convince Gotelli to get medical and psychiatric help in which Gotelli decides to throw in his badge for good. Meanwhile, Simone's continuing help with the FBI makes his life miserable when the men from Internal Affairs investigate him for the government license plate number on Salvo's car that he ran and is frustrated when he cannot tell them, not even Sipowicz, about what he's doing. Elsewhere, Sipowicz and Simone investigate the beating and murder of a woman in her apartment and deal with the emotionally sensate superintendent of the building whom they think he knows more than he's telling them.

Simone and Sipowicz investigate the murder of a man where the only witness is an insane woman, who lands in danger after she is kidnapped by their suspect's lawyer. Meanwhile, Medavoy and Martinez investigate a string of taxicab robberies which leads them to the brother of a gypsy cab driver. A new administrative aide, named Naomi Reynolds, arrives to substitute for Gina's absence.

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.

Kirkendall's son witnesses the murder of a convenience store clerk. Medavoy and Martinez investigate the death of a homeless man.

John Irvin fears the worst when Dolores disappears. The detectives search for a body when a mentally ill man confesses to raping and murdering his girlfriend's daughter. Two brothers run their own investigation when their sibling is murdered.

James passes his sergeant's exam. Jill's ex-husband could be causing problems for Jill.

Andy and Danny reopen an unsolved murder when the body of a small child is found buried within a wall; Medavoy and Jones deal with the owner of a dog who has a bullet in his nose they need as evidence in their case.

Andy goes into a tailspin when a doctor's visit reveals that Theo may have cancer. Diane and Jill's relationship suffers when info about Jill's ex-husband surfaces. Andy and Danny ponder the impact on Jill's career.

Fancy is being sent on a training course ahead of the squad getting computers. A woman is attacked by a court jester in a hotel room, then a body is found in another room - are they connected? Diane questions her involvement with Danny.

A man loses his penis. Fancy makes Captain and the incoming Lieutenant is a ball-breaker. Andy is having second thoughts about Cynthia. A mob hit-man sings like a canary and implicates a celebrated Customs officer.

Sipowicz and Sorenson investigate the murder of a drug dealer, while Sorenson continues to see the stripper, Kristen, who draws him into a favor for the owners of the Tailfeathers club.

The squad investigates the murder of a young Chinese girl along with an alleged rape case. Irvin learns his father is dying. Clark tries to find a foster home for James Kilik.

A boy on a bicycle is murdered. Connie's sister posts bail for her husband.

The murder of a man who frequented a betting parlor leads Sipowicz to an old friend; Jones searches for the man who attacked Haywood; the detectives research the Colahans' background.

When another woman is murdered by the serial killer, the detectives arrest a suspect... and discover the killer's identity; and expecting a baby, Sipowicz and McDowell decide to get married.

Teacher David Lewis comes into the squad-room to talk about Cindy Clifton and a support group that he ran that she was a part of. Sipowicz and Clark let him go but send off some of his left behind chewing gum to DNA for testing. Jones goes to court as its the day when Michael is to testify against his father. Ortiz and Ronson go to the scene where tourist Ned Applebaum has been mugged and lost his wife's $35,000 necklace. Ortiz and Ronson eventually find out that Ned met a lady friend on the Internet and he was going to meet her in Little Italy when he was mugged. He was going to loan her the necklace so that she could use it as collateral for a loan for her sick child. The detectives get the PO Box number where Applebaum had sent previous gifts to his lady friend. Ortiz and Ronson go to the apartment of the owner of the PO Box. He is a day trader/con artist who they discover took advantage of Ned Applebaum. They get the necklace back and Ned is forgiven by his wife. Later, Gibson tells Sipowicz and Clark that David Lewis was found DOA in his apartment. They go to the scene and try to determine whether the death was a suicide or not. Sipowicz tries to decide how to proceed with the investigation of Lewis's death; both he and Clark believe that Brockhurst might be involved. Clark gets a call about Dr. Jennifer Devlin and goes to the hospital. The doctor tells her she needs to remain restrained for now, but he is allowed to see her as long as he doesn't loosen her restraints. Sipowicz finds Brockhurst and tells him of his theory that he killed David Lewis. Brockhurst doesn't admit to anything, but tells Sipowicz he is going to be able to sleep tonight now that the case is closed.

Sipowicz and Clark investigate the stabbing death of a coffee-shop owner who was attracted to young girls; Ortiz tries to keep her cousin out of trouble; and Medavoy and Jones link a murder to a paralyzed police officer and his family.