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 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 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 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 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.

After Israel hangs himself, Sipowicz investigates a clue which is a bible verse that Israel pointed out to him, which leads Sipowicz and Simone to set up a complex sting operation to find out if the father of the murdered boy really was the one that set the whole Israel frame-up. Meanwhile, Medavoy and Martinez look into a doctor who is helping out the homeless by getting them a job with insurance benefits that he helps collect.

Sipowicz is visited by an old school friend who asks him to help talk to his daughter about the company she is keeping, which takes a turn when the woman's roommate turns up murdered and Sipowicz thinks that another one of his old high school friends was involved. Meanwhile, Medavoy and Martinez look into a case where a man is getting a lot of teeth that contain gold fillings and they uncover a small grave robbing operation. Simone overhears Naomi talking with a different accent, and she tells him that she is actually from Australia and about her desire to become a policewoman.

Simone, Sipowicz, and Russell investigate a shooting of two women and later go into a raid on a drug dealer's apartment in which Russell risks her life to capture the dealer/murderer, but later Russell tells Simone that she happens to be pregnant. Meanwhile, Martinez and Medavoy look into the murder of a prostitute, despite Martinez's complaints about a back problem that later gets him taken out of the squad. Also, Naomi tells Simone about her problems with her landlord who has reported her to the INS.

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.

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.