Martinez is shot in the back during a scuffle and the doctor's report is possible that he may be paralyzed for life. But Martinez's assailant, a government witness in a relocation program, will probably go free and Simone contacts reporter Benita Alden, his former girlfriend, to help put pressure on the D.A. to prosecute their protected witness. Meanwhile, Russell, on the road to recovery from her alcoholism, wants Sipowicz to let Simone know she's doing okay but she is on the brink of falling off the wagon. Donna expresses to Simone that she has feelings for him, and Sylvia tells Sipowicz that she may be pregnant.

Medavoy and Sipowicz go undercover as Hasidic Jews to recover a stolen Torah. Meanwhile, Simone gets a case where a father suspects his intellectually disabled son of killing his daughter. Detective Stuart Morrissey tactics with the suspect does not sit well with Lt. Fancy, despite the facts that the case match the one Simone are working on. Also, Sylvia visits a doctor who confirms that she's pregnant, and Lesniak keeps checking up on Martinez still in the hospital.

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.

Lesniak's preference of her lesbianism quickly gets around the precinct, which gives her mixed reactions. Meanwhile, Sipowicz clashes with Simone throughout their investigation of the senseless murder of two kids, which is only the start of a really bad day which also includes Sipowicz dealing with Sylvia's morning sickness, and Simone dealing with Russell who falls off the wagon.

Fancy is less than enthused when Ronnie Drucker, a detective under surveillance by Internal Affairs, is assigned to the squad and Simone is asked to keep an eye on him. Both Drucker and Simone work on a case where an elderly man has been accused of exposing himself to a young boy. Sipowicz, Martinez, and Russell investigate the murder of a pimp in a laundromat which is witnessed by a young homeless woman who turns out to be Holly, the teenage runaway who helped the detectives out on a previous case (from 'The Bank Dick' episode). Meanwhile, John Irvin asks Sipowicz if he should approach Lesniak to congratulate her on "coming out." But she won't listen to his gay pride talk as does everyone else.

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.

Sipowicz becomes annoyed when federal agents take over their investigation of the disappearance of a millionaire. Then a petty criminal from the past surfaces with information about the kidnapping and Sipowicz decides to act on it. Meanwhile, Simone aids an old boxer friend of his, who happened to got him started with bird breeding.

Simone and the men from Internal Affairs share the suspect after Simone gets some information from his incarcerated friend, Ray, about a case that Mike Roberts once worked on. Meanwhile, Fancy and Sipowicz both work on the case of a self-confessed gunman in a neighborhood shooting, once they get the story they help the shooter out. Medavoy investigates the assault case of an actor who was injured in a staged fight that went awry.

Medavoy and his wife, Marie, split up once again and she comes down to the station to have some hard words with Donna, while he decides to crash there since he cannot afford a place to live. Meanwhile, Simone and Sipowicz team up with Detective Harold Ng to probe the death of a Chinese girl whose leg has a strange marking on it which may have been self inflicted. Martinez and Lesniak look into the robbery case where a woman in a wheelchair lets a man claiming to be a policeman into her apartment, while the husband reveals a clue to Martinez that he has been seeing a prostitute on a regular basis and whose pimp might have planned the robbery. Elsewhere, Sipowicz does not want to accompany Sylvia to her latest doctor's visit, and Martinez gets an opportunity to find out where Lesniak really stands on her sexuality if she's really gay.

Sipowicz has race relation problems with the organizer of a local basketball game, held in the memory of a young boy, which erupted into violence by the gang members on the opposing sides which left two dead and seven wounded, and was witnessed by a reporter. Fancy has problems when Sipowicz racist colors come to light and has him removed from the case, much to his anger.

Simone and Sipowicz look into the death of a young woman whose body is found burned beyond recognition, except for a tattoo on her back. Detective Vince Gotelli arrives from another precinct to assist Simone and Sipowicz with their case and puts his two cents in, much to Sipowicz's delight and one of the victim's roommates becomes the prime suspect. Meanwhile, Medavoy pulls double shifts for himself (to get away from problems at home) and is assigned to watch an informant who has a penchant for playing poker with his friends.

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.

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.

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 makes contact with Ferdinand Hollie, an old informant, who wants to help him capture a pair of Colombian drug dealers who killed a young girl with their crossfire. But Hollie, a drug addict who is HIV-positive, has his own agenda to rob the Colombians. Meanwhile, Russell is paired with Sgt. Ray Kahlins, a "blowhard" from the federal anti-drug unit who is more interested in collecting overtime pay than catching a separate pair of drug dealers during a stake out. But Kahlins' brash tactics and disrespect for Simone and his informant Hollie, put both cases at risk. Also, Medavoy and Martinez investigate the murder of a Santería priest found in a local sewer and try to link a parole officer and a recent parolee to the crime.

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.

Sylvia confronts Sipowicz about her suspicions that he is going to late-night bars and drinking again, and the effect is everywhere. Lt. Fancy is forced to sent him home after Sipowicz walks in one morning drunk. Sipowicz even fights with some street punks, gets beaten up, and Simone offers to look for the men that beat Sipowicz up. Meanwhile, a new administrative assistant, named Lucy, arrives as Donna's replacement. Also, Russell investigates a young woman, named Angela, who claims to have been stabbed by her jealous boyfriend. Simone, following a lead from a streetwalker named Deena, finally tracks down and confronts the two thugs who murdered Andy Jr. and guns them both down in a hail of bullets.

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.