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.

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.

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.

An ex-con that Sipowicz put away a year ago approaches him and tells him about a prisoner who's been serving time for a crime he didn't commit and he and Simone decide to reopen the case. Meanwhile, Martinez wins the election by just three votes, much to Gotelli's chagrin. Simone comes across Detective Nick Savino who helps him with the investigation of the murder in his building and Savino suspects Henry has something to do with it. Fancy gets a cavity filling which makes him more edgy than usual and Medavoy loses one pound more than Sipowicz. Also, Russell still has not come to any conclusion about her relationship with Simone.

An African-American community activist, named Kwasi, with whom Sipowicz had a previous run-in, is found murdered in a drive-by shooting. Simone and Sipowicz investigate, and Sipowicz rekindles Fancy's and Kwasi's family's anger over the previous incident. Meanwhile, Martinez and Medavoy investigate a homicide at a bodega and have a hard time getting witnesses to cooperate.

Simone and Sipowicz investigate a case where two transvestites witnessed a murder that they say was committed by a 'gay-basher' who's supposed to have been in jail for a previous crime. Meanwhile, Fancy's former foster son is arrested and charged with possession of a kilogram of heroin. He tries to make a deal with Sgt. Ray Kahlins, the "blow hard" from the DEA who worked out of the squad room the previous year, to nab the drug dealers. Medavoy finally asks out Abby Sullivan, the beat cop from the anti-crime unit upstairs. But she turns him down by revealing that she is a lesbian. Elsewhere, Russell gets more deeper involved in her undercover work which puts a strain on her relationship with Simone. But the psycho Jimmy's malevolence puts Russell's life in danger when he puts a drug in her drink.

While tracking down Jimmy, who drugged and date-raped her the previous night, Russell works with Martinez and Medavoy on a case where a man with a muscular dystrophy was killed in a very tight knit community. Meanwhile, Simone and Sipowicz work on another murder case that may have been masterminded by a married couple. Also, Fancy wrestles with Captain Bass and knowledge of the fact that Simone is going to be promoted to Detective 1st Grade, and Sipowicz isn't.

A woman comes into the station to report that there's a bullet hole in her wall. The gun is found in Jimmy Liery's apartment and Simone arrests Jimmy, but has to let him go as there isn't enough evidence to hold him. Simone finds out that Russell unsuccessfully attempted to scare Jimmy by firing a shot over his head. Simone decides to remove Jimmy unlawfully by setting him up to take a fall. Meanwhile, Sipowicz is still angry at Fancy who thinks he held up his promotion. Following a tip from a young runaway teenage boy, named Marco, Medavoy and Martinez investigate the murder of an apartment building tenant. Also, artist Walter Hoyt (from ep. UnAmerican Graffiti) returns and wants the detectives help to get his paintings returned from some mob guys that he is a witness against.

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.

Simone and Sipowicz investigate the murder of a woman whose body was found naked in the trunk of a car in a junk yard which leads them to a pervert with a penchant for lookalike porn actresses. Meanwhile, Martinez and Medavoy investigate a man who was found dead with a severe blow to his head from a typewriter. Simone hires Henry to take care of a painting job in the tenement building, where Henry comes in complaining about a difficult tenant. The emotionally and physically scarred Gina returns to work (with a large vertical scar across her left face), and Russell is working through her issues with her family problems by meeting a counselor.

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.

Simone and Sipowicz get another case involving the shooting of a rap artist who refuses to cooperate with them in the identification of his assailant. Meanwhile, Abby tells Medavoy that she and Kathy are trying to start a family and asks him to donate his sperm to her so Abby will get pregnant. Officer Szymanski, the racist cop who pulled over Fancy, tells him that he thinks Fancy was one of the ones responsible for his being set-up and caught in the alleged theft of a drug dealer's money. Also, Simone is approached and propositioned by FBI agents to help them with their ongoing investigation into the affairs of mobster Joey Salvo. Elsewhere, the night shift detective, Vince Gotelli, tells Simone and Sipowicz about a heart medical condition of his.

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.

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 returns to work at the 15th Precinct and immediately helps Sipowicz with his case of the shooting death that occurred during a robbery at a local bar. Meanwhile, Martinez and Medavoy stake out a hotel where a serial rapist has been committing his crimes. Gina finally accepts James' proposal and wants a quick wedding.

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 a break-in of a high-rise apartment where the wife and baby are killed and the husband injured. Vince Gotelli, now an insurance adjuster, tells Simone and Sipowicz that the man may have faked a break-in to kill his family to collect an insurance policy. Meanwhile, Fancy gets some clues about a 15-year-old unsolved murder case from a visiting old friend who is dying. Also, Russell, Martinez, and Medavoy investigate the murder of a record company executive who wasn't very popular among his co-workers.

Simone and Sipowicz investigate the disappearance of a young boy, who turns up dead and the father points that a mute homeless man, named Israel, may have been the one. But Supowicz suspects that the father may be the real culprit. Meanwhile, the rest of the squad investigate the murder of a Hasidic Jewish girl and have to juggle the need for their investigation against the needs for a quick burial.

Sipowicz returns to work after his successful prostate surgery, but apparently too soon, for he has an accident while interrogating a suspect. He is given desk duty to help Simone and Russell investigate the murder of a woman's boyfriend by her ex-husband, the ex-husband later revealed to be searching for his daughter who's gone missing while in the ex-wife's care. Meanwhile, Simone is called upon by Detective Nick Savino to help investigate a missing persons report that is being filed by the nephew of one of Simone's apartment tenants. Based upon past exchanges between the missing woman and Henry Coffield, another building tenant, Coffield becomes a suspect. Former administrative aide Naomi Reynolds shows up at the station, now wearing a private security uniform and speaking in her natural Australian accent, to visit Simone, hoping to tell him that her situation with the INS was resolved and she is now furthering her pursuit to one day become a NYC police officer.

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.

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.

Mike Roberts is found dead. John reveals a connection between Roberts and Cullinan, who was with Dolores when she died. Mike left behind a memoir detailing some of his work. Jill goes undercover as a drug-addicted hooker.

Dornan causes problems at an AA meeting and Andy asks the Lieutenant to talk to him. Dolores' father accuses the squad of withholding information from him about his daughter's murder. Jill splits from Cohen.

ADA Costas prepares for the trial against Cullinan, and chooses Sorenson to testify over her husband. A man is shot dead in his apartment, and his wife's story about Latinos looking for drugs doesn't add up.

Tensions mount as the Cullinan trial approaches. Mike Shannon brings a problem to Sorenson. Danny kisses Diane. There's a shooting at the courthouse.

The detectives investigate a multiple homicide at a fast food restaurant; an addict gives his 5 & a half year-old daughter to a drug dealer as collateral on an overdue loan; Internal Affairs reopens the Kirkendall case.

Danny wakes up in Diane's bed. Andy and Katie get Theo's test results. A former colleague of Bobby's reaches out to Diane from prison. The team investigate a series of cab-driver shootings.

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.