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.

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 Russell investigate two stickups held at ATM's where they get a line on a possible suspect and then use Kirkendall to appeal to the suspect's mother to help them reach out to him. Meanwhile, Medavoy attempts to sort out a case where he can't determine if there really is a twin when a man comes to the station to report that his twin brother, Pete, has threatened violence against his former girlfriend. Also, Sipowicz contends with a medical problem involving his prostate while helping Simone and Russell and he is less than forthcoming with what his doctor has told him about his condition. Also, a new administrative aide, named Delores Mayo, comes to work at the 15th Precient as Naomi's replacement.

Simone and Sipowicz try to conduct their investigation in the midst of racial turmoil in the station and the neighborhood when a young white teenager is murdered in a black neighborhood during a drugs-for-guns deal that went bad, and the victim's racist father comes to the station and begins quarreling with Lt. Fancy over his race and roll in the investigation. Meanwhile, Medavoy and Kirkendall investigate the strangulation and dismemberment of the mother of a young boy, who's discovered his mother's body in the refrigerator. Also, Russell decides to take some time off since she's feeling ill due to pregnancy morning sickness, only to suffer a miscarriage at the end.

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.

Richardson confronts Sipowicz and Simone about their impending questioning of his wife over the murder of the nurse, but with the exception that Richardson is a real bad person, Sipowicz and Simone reach nothing. In a cross-over from the series "Upstairs", former temp and private detective John Irvin stops by the station to tell the detectives about the new graphics art business he started. But with the exception of the receptionist Dolores, no one is around, including Medavoy who leaves in a hurry for upstate New York where Abby now lives to be by her side when she goes into labor. Meanwhile, Kirkendall and Russell look into the theft of a graduate film student's camera, where only the student seems more interested in dispensing his own justice. Also, Sylvia finally learns about Sipowicz's medical condition from his doctor and finally persuades him to go for further tests and possible surgery.

Simone and Sipowicz look into the shooting of two women (one of whom was killed) who were raped by a group of men in an apartment owned by a former crack dealer, named Jamal, who was crippled in a previous shooting incident. Sipowicz confides in Simone about his medical condition when Simone sees Sipowicz's doctor pull him aside and talk to him confidentially. Meanwhile, Kirkendall, Russell and Medavoy investigate a shooting at a clinic. When they get a woman suspect into custody, a security guard from the clinic who was her secret admirer comes to the precinct demanding she get a second chance.

The detectives get a break in a case involving a police officer suspected of committing murder.

As Sipowicz prepares for prostate surgery with Sylvia by his side, James Martinez returns after recovering from his back problem where he reports that Gina had her baby three weeks earlier. But Medavoy is even happier after returning from upstate New York with a videotape of Abby giving birth to her baby and is very eager to show the tape to anyone who will watch. Meanwhile, the rest of the squad gets involved in a case of five reuniting Army buddies when one of them is found dead. The four others try to keep their fabricated story straight as Simone and the others try to figure out their involvement.

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.

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.

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 the torture-murder of a hotel magnate's son. Russell and Kirkendall suspect that an attempted rape victim is hiding something. Simone's health begins to deteriorate.

The detectives of the 15th Precinct investigate a double homicide involving one of their own, an alcoholic cop who seems to have done the right thing, but can't remember key details about the incident.

The detectives question a group of unsavory suspects after a well-dressed man is found dead in a park. The squad tries to stay optimistic as Simone is told that he will require a heart transplant.

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

Sipowicz helps his ex-wife deal with a drunk-driving violation. Simone's body rapidly succumbs to infection in the wake of his heart transplant.

Youthful detective Danny Sorenson joins the squad and, during a multiple homicide investigation, discovers that his new colleagues have yet to recover from Simone's death.

Sorenson and Sipowicz investigate the beating death of an elderly shop owner. Russell and Kirkendall encounter Dolores while investigating a homicide at a strip club.

The detectives search for the truth when a white off-duty police officer with a history of racism fires upon an African-American undercover cop. Dolores is arrested for shoplifting.

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.