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.

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.

A young boy is suspected of killing his mother's boyfriend; Fancy realizes that Lt. Abner is severely depressed. Sipowicz has a date with a niece of a friend as a favor; Katie becomes upset at this news.

A schoolgirl is found dead. Andy asks Eddie's niece on a date. John babysits Theo for the first time.

Danny is restored to full duty. Off. Szymanski's cousin is knocked down in the street and killed. Capt. Bass's wife is injured during a robbery at her store. Greg plays matchmaker.

Andy witnesses a hold-up in the street and shoots at the get-away car. Det. McDowell is assigned to fill in at the squad again.

A man caught carrying a cash register takes Andy and Danny to a body. Fancy is packing up to leave. His replacement alienates the squad before he's even left.

Rodriguez mediates when Sipowicz and Sorenson clash with detectives from another squad anxious to solve a multiple murder case; Medavoy and Jones try their hand at making extra cash by cleaning up murder scenes.

The squad investigates two homicides: the immolation of a would-be musician and the stabbing of a socialite. The newest detective to the squad, John Clark, Jr., attempts to both learn a new job and fit into the squad despite interference from his father.

The squad is joined by Eddie Gibson who's been transferred from nightwatch. McDowell and Gibson investigate the murder of a woman with MS, while the other detectives investigate the killing of a Rikers corrections officer.

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.

The squad investigates the theft of a baby from a hospital, and the arson of an Arab-owned business.

The squad investigates the murder of two drug dealers, and the discovery of a body mistakenly listed as a victim of the World Trade Center attack. McDowell arrests the daughter she gave up for adoption.

Sipowicz and Clark investigate the murder of a hispanic worker, while Medavoy and Jones search for a puppy-knapper who stole valuable champion bulldog pups. McDowell gets a new partner--Rita Ortiz.

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 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.

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 the shooting death of a jogger who'd been having an affair with a police officer; and Medavoy and Jones search for answers when the body of a comedy club owner is found in the trunk of a stolen car.

A new detective, Stan Hatcher, joins the squad; the detectives investigate a shooting death that Hatcher believes is linked to a dispute between gang members; and a man insists that his young daughter has been kidnapped.

A kidnapping victim's startling statement clues Andy and John in on a serial sadist keeping women locked in a dungeon somewhere in New York. Meanwhile, a routine robbery investigation takes a saucy turn for Medavoy after he makes an unlikely connection with the 60-year-old victim.

Sipowicz searches for the truth when Hatcher is shot by a man who mistook him for a burglar; and a former pharmacist dies in a flophouse when someone fires a bullet into his room.

Andy's off-duty and slightly underhanded work to prove that Hatcher killed his own wife lands him a transfer out of the 15th precinct and into the Bellevue Morgue engineered by Detective Hatcher. Meanwhile, the squad is up to their whips and chains after a dominatrix is found murdered.

Haywood reopens an 18-year-old case that has Andy reliving a major mistake in his career. Meanwhile, Sipowicz and Clark investigate the death of a man whose brother was pursued by a bounty hunter. Elsewhere, Ortiz gets a new partner, Detective Kelly Ronson, who ends up lending an unusual hand during the hunt for the child an ex-con had to give up before going to prison.

A man's gunshot-induced amnesia causes Jones and Medavoy to concoct an unconventional way to nail his assailant. Meanwhile, a man Sipowicz put away twenty years ago for raping and murdering a 12-year-old girl goes free after DNA testing exonerates him, and Ortiz and Ronson bust a gruesome underground network pre-teen prostitution ring.

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.

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 investigates a murder involving the victim's current husband and ex-husband; a longtime informant gives Ronson information about an illegal gun shipment, but the suspect's father is being followed by the FBI; Jones gets into a fight with Craig after he's acquitted of murder charges; and Sipowicz is the proud father of a baby boy.