A shady homeless man, named Lou, comes to the station thinking he's a werewolf and demands to be locked up into a cell before he kills someone when the night comes. However, things take a turn when Kelly investigates Lou when he may be a witness in the murder of a nine-year-old immigrant boy. Meanwhile, Sipowicz is visited by his long-estranged son, Andy Sipowicz, Jr. with his fiancée, Patty Constance, an older woman who Sipowicz discovers that she has been cheating on Andy Jr. Elsewhere, Giardella is killed in his hotel room by a Mafia button man dressed as a window washer before he can testify to a grand jury against his superiors and Laura finds herself the only witness to the murder.

After Robin's husband dies, she gets angry when his will seems to stipulate that Kelly should resume his duties as her bodyguard. Meanwhile, Sipowicz must clear his own son of a drug pushing charge. While investigating a tip on the location of a dead woman, Medavoy, Martinez and Kelly find another body of a dead man in a garbage dump which leads to Kelly suspecting a hotel concierge and the hotelier of conspiring to murder the hotelier's husband.

Kelly gets an ultra-high priced mob attorney to defend Janice on the double murder charges and helps out with her bail. Meanwhile, Sipowicz tries to make amends with Sylvia who's been attending Alanon meetings. While helping with Andy Jr. look for a new car, Sipowicz comes across a lead in a disappearance case that has frustrated him for the last 2 1/2 years. An old Ford van which may have been used in an abduction re-surfaces at the lot. Elsewhere, Kelly investigates the murder of a priest and later meets with Robin for a lunch date and spends the night with her.

Lesniak deals with a perpetrator and his "high priced lawyer and shrink" when he repeats the offense. Meanwhile, Detective Solomon uses a fast pull to take a possible serial killer case away from Simone after he brings in a possible suspect. One of Fancy's old contacts, Vinnie Greco, brings in a tip about a couple of guys looking for some heavy arms to do an armored car job and Sipowicz works with him, but Greco is working for someone else against Fancy. Sipowicz invites Andy Jr. over at his place for dinner where his son tells him that he is joining the Air Force. Also, Sipowicz proposes marriage to Sylvia and this time, she accepts.

Pre-wedding jitters put Sipowicz in a rare form of panic whereas Sylvia remains perfectly calm. While investigating a murder in Chinatown, Russell's drinking problem makes her miss getting a gun off a suspect and she finally admits to Simone about her alcoholism. Meanwhile, Fancy's brother, Reginald, is still having problems with his racist sergeant and his belligerent attitude has resulted in him being investigated by Internal Affairs. So Fancy, Simone, and the squad work together to help clear Reginald of any misconduct. Martinez finally goes out on a date with Lesniak and asks her to be his date for the wedding. At the ceremony, Simone is Sipowicz's best man, Sylvia's father escorts her down the aisle and even Andy Jr. makes it just in time for the ceremony. Medavoy brings his ex-wife to the wedding while a lonely and jealous Donna painfully watches from afar.

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.

A detective from another precinct, Martina Escobar, joins Simone and Sipowicz with their investigation of a rapist/murderer who is throwing small children from the tops of buildings. Meanwhile, Martinez and Russell investigate an alleged case of date rape, but the women of the squad and Sylvia have a major disagreement with Martinez's decisions regarding the suspect. Elsewhere, Sipowicz shows his son the ropes of being a cop.

Simone and Sipowicz help a local FBI agent, named Mike Frances, to investigate the murder of a local Italian mobster. However they are forced to commit robbery while working undercover for Agent Francis, and have to place a bug in the mob hangout. When two wise guys come to the station to file a robbery complaint, Russell and Medavoy catch them in the act of filing a false report. Meanwhile, Donna's hairdresser, Marina, tells her that she has a problem with her ex-boyfriend. He wants to hijack Marina's current boyfriend's truck, and Martinez goes undercover as Marina's boyfriend. But Lesniak is unable to hide her jealousy and possessiveness. Elsewhere, Andy Jr. learns more about being a beat cop with more pointers from his father Sipowicz Sr.

Sylvia is now nine months pregnant and ready to give birth any day so Sipowicz is on the edge. Meanwhile, Simone and Sipowicz, with Andy Jr. along for the ride, investigate a case where the drug-addicted nephew of the victim of a robbery-homicide is found holding the stolen goods. Meanwhile, Medavoy, Martinez, Lesniak, and Russell all join forces to work on the robbery-murder of a bouncer where the leads first lead to a biker, then to a check cashing forger, and to his co-worker. In the mist of the investigation, Martinez and Lesniak finally reach an agreement that they are not right for each other and quietly break up by agreeing to try a platonic relationship. Also, Donna contemplates an administrative job offer in California.

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.

Fancy and his wife are pulled over and harassed by a racist police officer for a burned out taillight, and he and the precinct commander, Captain Bass, don't see eye to eye on the procedures followed during the stop. Meanwhile, Sipowicz has some unresolved issues to work out Andy Jr.'s death when he begins having a string of dreams involving his late son. At the same time, Sipowicz works with Simone on a rare night duty and gets a case involving trying to find the perpetrators of a bar robbery, while Simone locks horns with the conniving Detective Eddie Hazell who is seeking to derail Simone's investigation to take the credit for nabbing the robbers all by himself. Also, Medavoy, Martinez and Russell work together on a sting operation to catch two female con artist investors defrauding old and crippled women.

Andy goes into a tailspin when a doctor's visit reveals that Theo may have cancer. Diane and Jill's relationship suffers when info about Jill's ex-husband surfaces. Andy and Danny ponder the impact on Jill's career.