Simone and Sipowicz investigate the race-related murder of a Puerto Rican teenager who was attacked while spray painting graffiti in Little Italy. Meanwhile, Medavoy meets Donna's former boyfriend, Harold, when he comes to the station to file a car vandalism report, while Donna makes a tough decision about her relationship with Medavoy. Also, Sylvia is mugged and she later tells Sipowicz a secret from her past about being raped as a teen.

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.

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.

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.

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.

Medavoy decides to go on a diet and has a hard time getting started on it. Meanwhile, Sipowicz has problems with his work, his baby son's illness and Sylvia deciding to return to work at the D.A.'s office. Simone proposes marriage to Russell, but she is hesitant to give him an answer. Martinez has eyes for Gina Colon the new administrative aide for the anti-crime unit since Lesniak has been transferred from the squad to another precinct, thus leaving the 15th for good. But none of the men are turned on by Donna's latest replacement, a frumpy lady named Gerri Turner as the PAA for the squad but she has a strong interest in Sipowicz. A body in a trunk of a car is inadvertently moved from the nearby 13th precinct into the 15th's jurisdiction. Elsewhere, Simone inherits an apartment building from a recently deceased woman and the woman's son, Henry, is upset at the situation.

Simone and Sipowicz investigate a murder, but the procedures they must follow make them unpopular at the precinct when a fellow cop might have been involved. Meanwhile, Medavoy and Kirkendall investigate the murder of a young girl where the only clue is a videotape that starred her crushing worms. Russell goes missing and eventually turns up in Simone's apartment where she recalls to him that her father molested her as a child.

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 and Sipowicz investigate a shooting that is related to the victim trying to leave a street gang. Meanwhile, Kirkendall and Russell investigate the death of a baby who appears to have been shaken to death by the baby-sitter. Medavoy and Martinez look into a murder at a garage where they have a suspect who looks guilty despite the fact he claims to have an alibi. That evening, Medavoy has dinner with Abby and her lover, Kathy. Also, Simone takes Russell out to a movie and proposes to her again, and this time she accepts.

In the four months since Joey Salvo's assassination, Simone is working odd jobs since he has been suspended by Internal Affairs pending their investigation, while he approaches Sipowicz asking about his and others incitements by the FBI who think that Salvo's death was an inside job within IAB, and Lt. Shannon from IAB tells Lt. Fancy that he may know the person who killed Salvo. Meanwhile, Gina discovers herself to be pregnant, but is hesitant on telling Martinez.

Simone and Kirkendall work on a murder case where a son is bitter about his father's death and offers $5,000 to anyone who can produce the killer, and the result is a greedy horde of people with many false leads. Meanwhile, Sipowicz and Russell investigate the rape of a nine-year-old girl, whose mother thinks the culprit may be a retarded boy from their apartment building.

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 a crime where a man discovers a woman's body stuffed inside a large box. While on the case, they meet the victim's brother, a strange man who is more concerned with drinking a particular brand of soft drink. Meanwhile, Russell investigates the death of a child whose parents do not seem fit to raise a child. Also, Kirkendall and Medavoy look into the death of a young boy whose very religious parents suggest that the person who killed their son can be forgiven.

A murdered couple is found where the dead man is a car salesman and the woman is a prostitute. Simone and Sipowicz look into the salesman's death, while Medavoy and the other detectives look into the prostitute's death, where the M.O. of the suspect is to buy used condoms from a prostitute and then mix the spent semen with his own to cover his crime. As Sipowicz recovers from his surgery, he finds that a recent blood test is not favorable and once again keeps his medical problem to himself.

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

Jill's son has his first communion, where Andy and Danny spot a surveillance van across the street from the church. A baby is found dead in a dumpster.

The squad attends a homicide with seven naked bodies. Jill's ex is arrested.

It's James' last day with the squad before he moves on as a sergeant. Jill's ex is in the wind and causing more problems for Jill.

Medavoy gets a new partner. A cop is shot and killed. Diane seeks counsel from Andy about whether to tell Jill what she knows about her ex.

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.

A homeless guy Danny was trying to protect turns up dead. The DOA's father is concerned about the trust fund his sister will now inherit.

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.

Jones and Medavoy investigate the murder of a Chinese restaurant owner. An IRS lawyer claims to have been kidnapped and released, but Sipowicz and Sorenson doubt his story.

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.

Sipowicz, Clark, Medavoy and Jones investigate the murder of an unassuming teenager. McDowell and Ortiz search for the person responsible for firing a stray bullet that killed a three-year-old girl.

The detectives work to solve two murders: the shooting of a rising rap star and the shooting of stripper found nailed to a table. McDowell and Sipowicz try to define their relationship.

Andy and Connie return from their week's holiday with Theo. A boy goes missing, and the squad is lead to a pedophile in the area. John meets with a lawyer about his father's estate.

Connie struggles to settle with the baby. A woman is found dead in a vacant lot. Another is found dead in the laundry room of her building. The Lieutenant dresses up for a lunch.

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.

Jones accidentally shoots a 13-year-old boy while pursuing a murder suspect; McDowell and Ortiz search for answers when a man whom police escorted from the scene of a domestic dispute is found dead.

As Andy and Connie prepare to finalize the adoption of baby Michelle, Frank Colahan's mom and dad show up. Connie sweetly and sincerely tells them they want the grandparents to be part of Michelle's life to the fullest extent possible.

A woman survives the serial killer's attack, and her account prompts the detectives to focus on Carlin, his partner, and a bodyguard; Medavoy and Jones investigate when an off-duty officer kills a man; and McDowell comforts Russell during a biopsy.

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 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.

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 investigate the death of a phone-sex operator and the kidnapping of a wealthy man's son; and Clark's tryst with a murder suspect is used to derail the prosecutor's case.

A gunman tries to kill a witness after a mistrial is declared in the Simon Kerensky arson case; and Jones goes to extremes to stop Craig from adopting Michael.

As he begins his new job as squad commander, Sipowicz disobeys orders and keeps a murder investigation open... even though a Japanese man with diplomatic immunity has confessed to the crime.