A violent criminal shoots a police officer outside his station and then goes on a rampage. A chase erupts through the streets ending with numerous wounded and dead. The criminal is captured and dragged into the station, because there is also a sniper shooting at the police, where he consequently dies. Did he die from his wounds or was he beaten to death by the cops?. His sister and a priest want to know the truth, and are determined to find it.

The repercussions of Hopkins' death (the violent criminal from the pilot) in the station continue as the Internal Affairs department investigate and Hopkins' sister brings in her own lawyer to find out who 'murdered' her brother.

A Hacidic Jew and his grand daughter are mugged. A militant Jew organizes a vigilante group to find and punish the assailant, believing the police will never find him. Lt. Jonas interrogates Jack over the death of Hopkins in custody.

The O'Donnells' father is murdered, the son thinks he was killed by one of the Westbrook boys, their next door neighbors and constant adversaries. Jack has to go to a grand jury over his alleged participation in Hopkin's death and has to wait to see whether he still has a career or not.

A woman comes into the station to report that she is being harassed by a group of clowns living next door to her. She tells them that they make too much noise all through the night and can often be seen participating in orgies through their windows. A disabled man is beaten up and robbed in his own apartment. Jack and Nona try to help him out and recover his precious stamp collection. A collection built up over the years and full of memories.

Santoro's brother-in-law is arrested for possession of stolen goods, kept in a lock-up that has Santoro's name on the lease, which could cause problems for Santoro. While visiting an apartment on official business Clem, Phil, Doyle and Hector hear shots coming from the floor above and chase the perpetrators to the roof. One is killed but the other gets away. They killed a family because drugs were being dealt from their apartment. The view of the officers is that it was more than a random occurrence and that a recently paroled drug lord, Jerome McFee, was involved in some way.

Two gay men are arrested for brawling in the street. By the time they reach the station house their injuries seem to be much worse and one of them accuses the two officers who brought them in of police brutality. Terry finds himself doing some driving, to earn some extra money, for a businessman. He informs his brother, and then IAB, of this when he discovers that the man is a major criminal and is asked to go undercover, even though he hasn't even finished at the academy yet.

Terry begins his undercover assignment. Kevin Patrick has trouble coming to terms with his disabling injury and Jonas takes up his new post. A badly wounded woman leads the precincts street cops to a house with six dead bodies, all tied up with their throats cut. The investigation starts to find those who committed this crime.

The ex-wife of McKenzie, the prosecutor who helped Jack, is found dead in her apartment. 'Woody' is the main suspect and the detectives investigating think he may have hired a killer. Looking for help he calls Donovan to help him. Terry gets deeper into his undercover role and Jimmy finds out that the Irish gang involved is setting up a deal to buy automatic weapons.

Terry's undercover work is beginning to worry Jimmy. Joe has it in for Terry, because Jimmy arrested him when he was younger. The bank job is going down soon and Joe could be planning to set Terry up. Kevin Patrick comes back to work, trying to adjust to the fact that he is going to spend the rest of his life in a wheelchair.

Heagan's disciplinary hearing, over the gay beating, takes place and Phil has to testify against him. Even so with Pittorino now changing his testimony it looks like he could go free. Officer Anthony Fiano shoots and kills an armed robber while in a gay bar. When he comes in he is questioned by Det. Hayes and an IAB Leut who seems determined to take Fiano down, or at least get him to admit that he is gay.

A young girl has a man expose himself to her near her school. Her father is a court officer and an old friend of Captain Jonas'. He wants something done about it and asks Jonas to make sure his men find this pervert. As the number plate of the suspects car was taken this is easily done but the girl cannot positively identify the man. Without any evidence the man is freed, much to the father's disgust. Not long after this Jonas is personally called to a crime scene where his friend is found, with the dead body of the released suspect. Terry starts work in anti-crime, partnering up with Christine Bannon.

Clem and Hector arrest a prostitute for possession of drugs, Hector recognizes her as being one of the clowns arrested previously and wants to help her, against Clem's advice. She wants to give up the name and address of her supplier for her freedom. No one is quite sure whether or not what she is telling is the truth but agree to look into it anyway. Jimmy is partnered with Ray MacElwaine, a new officer just transferred in from another precinct, investigate a number of robberies involving the theft of collection jars for a home for alcoholics.

Jack plans to marry Elena, an eastern European woman he met a short time ago, to help her with her immigration problems. Members of an opposing gang raid a hospital to try and kill an already wounded member of another gang. To stop an all out war between the two gangs the precinct make arrests and then arrange a sit down talk between the two gang heads. A lawyer sues Phil and Ann-Marie for, among other things, allowing a suicidal woman to leap from a building onto his car.

After Jack and Clem get into a fight over Elena and Nona the hostilities between them rapidly grows. Santoro finds himself in trouble after trying to help his brother-in-law with a bookie problem.

Donovan is forced to reveal his secret work to the rest of the precinct before it becomes common knowledge. His fellow officers have differing reactions to this news. A landlord gets help from the precinct to evict his tenants. He wants to turn his building into expensive lawyer apartments. When one of his tenants gets a court order allowing him to stay they officers know that trouble is sure to start brewing very soon.

Donovan's dad comes back to town for heart surgery, having not even told his son that he had had a heart attack. Nona goes undercover as a prostitute, eliciting a number of comments about the way she looks from her colleagues and Phil has trouble staying awake during his shift after working nights as a security guard at a mortuary so that he can buy his mother a car.

Elena, Jack's ex-girlfriend, is found dead in an alley, shot three times. The prime suspect is a Latvian businessman who she had often been seen with in a coffee bar. Santoro is asked to help out his nephew with a few speeding tickets and ends up losing his temper with the highway cops and insulting them. Doyle and Ray keep being called to the apartment of a couple who are continuously fighting.

A man comes into the precinct station to tell the sergeant that his boyfriend has a gun to his dog's head and is threatening to go on a rampage. Ann-Marie is asked to go undercover as a rich widow trying to buy drugs, a supposedly easy job that goes badly wrong. Nona and Jack spend her birthday together.

Ann-Marie starts her first day as a detective and begins by organizing a raid on an apartment where an informant has told her two men are making bombs. The precinct gets a new PAA, someone Phil remembers from his old precinct. He tells Santoro that she has a obsessive compulsive disorder that involves cleanliness and having to do everything four times. She is so annoying that she is always getting moved from station house to station house.

An arrested drug dealer dies in a cell in the station house. The coroner determines that he died from strangulation, which puts Doyle in a jam as he was the arresting officer and was supposed to have kept an eye on his prisoner. Clem is approached outside a supermarket by a man who has a plan to scam the business' owners. A sting is set up to arrest the man but things do not go according to plan.

A member of the Latin Queens, a female gang, is found dead in her apartment building. Suspects are brought in, including a member who has been working undercover for two years. Ray arrests a man who throws Hector over a bar and injures the man's ribs while doing so. They take him to hospital where a doctor is amazed at the injuries he has received.