Russell, on the road to recovery, wants Andy to let Bobby know she's doing okay now. James is shot and may be paralyzed for life. His assailant, a government witness, will probably go free. Donna expresses her interest in Bobby to him. Bobby contacts Benita to use her to help put pressure on the DA and their protected witness and they talk about their time together. Everyone wants Bobby, but he has still feelings for Diane. Sylvia has some news for Andy.

A father suspects his retarded son of killing his daughter. Simone and Sipowicz get the case. Lesniak keeps reporting on James' condition. Morrisey's tactics with a suspect in a murder don't sit well with Fancy; however, the facts in this case match Andy & Bobby's case. While Simone and Morrisey work out the details of their combined case, Andy and Greg pose as Hasidic Jews to recover a stolen Torah. Sylvia takes another test (results positive) and asks Andy to be discrete. Later she discovers his level of discretion.

Medavoy and Lesniak pair up to identify who's launched a series of vicious attacks on a man. James returns to duty. Simone spots a possible suspect in a series of rapes. Russell tries to maintain her sobriety and it is tested when her parent's domestic problems get out of hand. Lesniak makes it clear to Medavoy she likes James as a friend only, and tells him she is gay, which he tells to James.

Lesniak's preference gets around the precinct. Sylvia's morning sickness, Russell falling off the wagon & calling Bobby, not him, and the senseless murder of two kids makes it a really bad day for Andy. Bobby and Andy clash throughout their investigation.

Fancy is less than enthused when a detective under surveillance by IAB is assigned to the squad. Bobby is asked to keep an eye on him. They pull a case where an elderly man has been accused of exposing himself. Later the man is found hanging out in his apartment on the door. The murder of a pimp in a Laundromat is witnessed by a young woman who helped the detectives out on a previous case. Andy debates about whether to let John cut his hair, when he does John asks him about whether he should approach Lesniak. When he does, she finds out that gay people don't listen either. The IAB plans to apprehend Drucker in the squad room.

An Indian woman is found dead in a car and Andy is full of theories about who and why. Donna is off at a computer course and her temporary replacement is a real character who clashes with Andy. James and Greg are nearby when a drug crazed man tries to rob a couple of stores of credit card slips. Russell and Lesniak work a case involving a man who was left to die of a drug overdose, that leads to a chance to nail a fence. Simone and Russell have words when she doesn't want him to provide the backup that she and Lesniak will require. Fancy has a couple of words for Bobby.

Sipowicz is annoyed when federal agents take over their investigation of the disappearance of a millionaire. Simone aids an old prizefighter friend, the guy who started him with birds, and who doesn't think he needs any help. A petty criminal from the past surfaces with information about the kidnapping, Sipowicz decides to act on it.

Simone and IAB share the suspect after Bobby gets some information from his incarcerated friend, Ray, about a case that Mike Roberts once worked. Fancy and Sipowicz both work 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 staged fight that went awry.

Greg and Marie split up again and she comes down to the station and sees Donna for the first time. Andy is also in the doghouse with Sylvia when he chooses not to accompany her for one of her tests that involves a large needle. Simone and Sipowicz probe the death of a Chinese girl whose leg has a strange marking on it. Martinez and Lesniak look into a robbery case where a woman in a wheelchair lets a man in who claims to be a policeman. Working together on this case gives James an opportunity to find out where Adrianne really stands in her sexuality.

A basketball game, held in the memory of a young boy, erupts into violence. 2 dead, 7 wounded. Andy has a race relation's problem with the organizer of the event that was witnessed by a reporter. Fancy and Sipowicz's relationship is on shaky ground as details of this event come to light and Andy is removed from the case.

Simone and Sipowicz look into the death of a young woman whose body is found burned well beyond recognition, except for a tattoo on her back. Gotelli puts his two cents in, much to Andy's delight. One of the victim's temporary roommates becomes the prime suspect. Medavoy pulls double duty (things still aren't good at home) and is assigned to watch an informant who has a penchant for playing poker with his friends. Unfortunately he might be put in a compromising position, when another ""player"" joins the game.

A woman comes into the precinct and gives Andy some information about a murder that may have occurred 8 years ago. Greg and Andy look into the situation, but question a lot of people who don't care that the victim is missing. Meanwhile a domestic violence situation in Russell's parent's apartment leads to tragedy. Bobby presses to get the truth and finds out what really happened to Diane's father.

Diane worries about her mother's pending grand jury trial. Andy and Bobby search for the killer of a mobster's son, which reveals a family affair. The lawyer of a suspect in a murder impedes Greg and Diane's investigation. The erratic son of the victim doesn't help much either and he has a thing for Diane. James and Adrianne get another shooting case that involves Andy and Bobby's suspect. The bullets are flying in NYC during sweeps' month.

Donna and Bobby give Adrianne and James advice, respectively, on their plans for their first night ""together."" Simone and Sipowicz investigate the death of a young woman who was brutally murdered. A surgeon's wife wants to press charges against her husband's mistress when her husband is shot. James and Adrianne spend the night together. Bobby and James go to Atlantic City to apprehend their suspect; Adrianne wants to know when he'll be back. Andy acts like a psycho in holding to get their suspect to drop his crazy story. James might be having second thoughts about his relationship with Adrianne.

A mild mannered professor is found decapitated in his apartment. James helps out a former porn star, who is getting harassing phone calls. I wonder what Adrianne thinks about that? Andy Jr. is in town with some surprising news, but he can't tell Andy about until dinner later that night. Andy worries about it all afternoon. Adrianne was not amused. Andy Jr., discharged from the Air Force, is joining the police department in Hackensack.

A rapist-murderer is throwing small children from the tops of buildings and a cop from another precinct joins Simone and Sipowicz with their investigation. The only thing Andy knows about this cop is ""she got her 1st grade money, the year I got screwed out of mine."" Martinez and Russell investigate an alleged case of date rape, but the women of the squad and Sylvia, have major disagreement with James' decisions regarding the suspect. Andy shows his son some of the ropes of being a cop.

Simone makes contact with old snitch. Martinez and Medavoy catch a murder case involving ""white magic."" Russell is paired up with a ""blow hard"" (who also knows Andy) from the federal anti-drug unit, who's more interested in collecting overtime, than catching dealers. Simone's snitch helps to capture the drug dealers who killed a young girl with their crossfire. The ""blow hard"" mentions where they got their information to their suspect. Andy and Bobby both have conversations with the ""blow hard"" about his use of his mouth.

Simone and Sipowicz are forced to commit robbery while working with an FBI agent to place a bug in a mob hangout. The wiseguys come to the precinct to file a robbery complaint; Diane and Greg catch the complaint. Andy Jr. learns more about being a beat cop. Donna's hairdresser has a problem with her ex-boyfriend wanting to hijack the truck of her current boyfriend. James goes undercover as her current boyfriend; Adrianne doesn't appreciate the competition. James and Adrianne have a talk.

Sylvia is close to giving birth and Andy is on edge. When isn't he? Donna contemplates a California job offer. The nephew of the victim of a robbery-homicide is found holding the stolen goods. Andy and Bobby (with observations from Andy Jr.) work that case. Greg, James, Adrianne and Diane all work the robbery-homicide of a bouncer. James and Adrianne have another talk. Sylvia gives birth with only a little trouble. It is a boy and they name him Theo.

A robbery-homicide sends Bobby and Andy to the hospital; however the victim is Andy Jr. Andy wants Bobby to lead the case and he also wants the opportunity for restitution. Diane doesn't like the way Bobby is handling the case. They turn up the weapon, but the suspects don't pan out. In the midst of all this turmoil, Donna makes the decision and quits her job. Andy goes for a walk and makes a stop.

Sylvia confronts Andy about his ""late night walks."" The new administrative assistant arrives to take Donna's place. Andy's return to drinking affects him at home and on the job, where Fancy sends him home. Bobby fulfills Andy's vendetta. A drunk Andy tackles some street punks, who get the better of him and his gun. Bobby and Officer Shannon work to locate the punks; Fancy gets the gun back; the rest is up to Andy.

Andy meets with Father Kankarides. Andy, Bobby and Diane investigate a holdup turned homicide. The new PAA isn't working out. Greg's on the verge of getting a new apartment. Upstairs John passes out farewell notices; he is going back to 1PP. Greg, James and Adrianne work a drug related double murder. Greg makes a new friend, Anne McGuire in anti-crime. Theo gets his introduction to God and Andy gets reacquainted. Bobby and Diane plan a trip to the shore.