The series concludes with the gangbangers taking out their assault on the 55th Precinct. After some grenade explosions, the precinct is destroyed. Cruz knows that Marcel Hollis is behind the attack, and she takes his life, as well as her own. Carlos proposes to Holly, and they are married. Everyone receives their reassignments, and Sully retires. In the last few moments, Sully narrates a look into the future.

The police officers sort through the carnage and count their dead in the wake of a shootout between rival gangs. While Faith tries to interrogate Fyodor Chevchenko, a ruthless Russian mob boss, Sully worries about the severely wounded Ty and regrets causing the incident. Tatiana chastises Sully for hassling her injured son. Faith worries about Gusler, her ineffective, frightened rookie partner and a weary Doc gets some unexpected, good news about his medical malpractice suit.

After a fierce gun battle and some hand-to-hand combat, Mann's gunmen are finally subdued by the members of the 55 in the E.R., but not before Orland is murdered and Bosco is critically injured; after Kim heroically puts herself in the line of fire to save Holly and a little girl, she realizes that her days as a paramedic are over, and that her future lies in being a wife to Jimmy and a mother to their children; Grace and Dr. Fields patch up their differences and come to an understanding about her out-of-protocol field procedures; Maritza uncovers the traitor in their midst, who leads her to Mann; Faith steps over the line to avenge her partner.

The deaths of four teenagers in a fiery car crash profoundly affects the third watch, who were forced to stand by helplessly, unable to save the victims. They congregate at the end of the shift to dispell their sadness and anger at the horrific images of the crash. Faith, Sully and Doc spend time sitting quietly in a cafe; Ty, Bobby, Carlos and Alex go to a bar; and Kim, Bosco and Jimmy go bowling. As evening turns into day, Faith's group meets up with a young woman, Ty's group meets up with a young man, and Kim's group meets up with a young couple in love. At dawn, everyone ends up at the a beach and they build a bonfire. As the flames flicker, we see a flashback to the moments immediately preceding the car crash and discover that the young people whom they met during the course of the evening are the spirits of the teenagers who died in the crash, who were sent back down to earth to tell them that the crash could not have been prevented, and they are not to blame for being unable to

On September 10, 2001, Ty and Sully are in Atlantic City on the eve of Sully's wedding to Tatiana. Kim sinks deeper into depression. Bosco searches for anything to do after someone lets out the result of the Giants game he had taped to watch after shift. Jimmy keeps trying to catch up on some sleep after nursing a sick Joey.

Bosco and Monroe investigate a suspicious man who they find bleeding in an alleyway as they respond to an anonymous caller's claim that someone is shouting for help in the area. They become more and more skeptical when his story continues to change and they find a blood trail. When it is determined that the amount of blood would have been more than enough blood loss to kill a person, Bosco suspects that the man murdered someone and was bleeding because the victim tried to fight back.

Faith negotiates the end of a live on TV hostage situation. The leader of a vampire cult holds Emily hostage until Bosco saves the day. Cruz attempts to negotiate a deal with a gangbanger to end the war on the 55th Precinct, but instead, he organizes his troops to attack.

Feeling betrayed, Doc angrily confronts his former friend, Jerry Mankowitz, an attorney's investigator who tricked him into confiding vital information about a pending malpractice suit.

Maritza's reckless pursuit of Buford triggers a horrific car accident that leads to multiple injuries to motorists, and triggers an explosion that severely injures Lt. Johnson and kills Alex Taylor; Doc and Kim get to the top of the promotion list; Maritza hangs Bosco and Nunez out to dry over the murder Noble committed; Doc's overwhelming guilt and grief over Alex's death leads him to a career decision; Maritza discovers that Faith has agreed to help Bosco clear Nunez by getting Noble's gun, and goes to Noble's place to intercept her, followed by Bosco and Noble; when Bosco insists on arresting Noble and Faith refuses to turn over the gun, Maritza draws on Faith, Bosco and Faith draw on Maritza, and three shots ring out.

Faith begs Fred to return home, but he refuses for a reason that infuriates his wife; Bosco turns a cold shoulder to Maritza's attempts to offer her condolences; Carlos is spectacularly unsuccessful in his attempts to hit on Grace; on the day of his son's funeral, Donald Mann exacts his revenge with the help of a dirty cop by planting bombs designed to kill the police officers he holds responsible for the death of his son; after Mann's lieutenants force a man to crash a car carrying a live bomb into the funeral home where Mikey's wake is being held, Grace takes charge and goes out of protocol to save Rose's life, and Dr. Fields later swears to have her job for it; Kim's decision not to enter the funeral home while the bomb is still live stems not from cowardice, but from maternal instincts; when Mann discovers that some of his intended targets survived the bombings, he sends machine-gun wielding minions into the hospital to finish off the job.

Bosco, Yokas, Sully and Davis search for a cop killer on the streets, and cope with an obnoxious new sergeant at the station house.

Ty, Sully, Bosco, and Faith rush to the scene of a school shooting; Sully and Tatiana ponder their future together; Kim continues to struggle with her depression.

It is September 21, 2001, and the squads continue to battle through their emotions and their misgivings about their hero status, while working double shifts and spending every free moment at "the pile" searching for the missing. Kim returns to work and teams up with Doc, which allows an emotionally frayed Alex to return to paramedic duty; an exhausted Sully attempts to co-exist with his prospective in-laws while he waits for an opportunity to marry Tatiana.

Steeper continues his by-the-books command style and goes head-to-head with Kim when Doc doesn't report for duty on time; Sasha can't find her off-duty weapon the morning after Doc's party; Faith returns to duty at the front desk despite Fred's wanting her to remain on disability, and discovers that Bosco has lied to her about Swersky's not allowing them to be partners; a panicky Nardo kidnaps Rose and then Bosco in a futile attempt to prove that he wasn't a rat, and makes a shocking choice when he realizes that his days as a mobster have come to an end; to the horror of the squads, Doc takes extreme measures to prevent Steeper from closing the house, and forces Carlos and Kim to risk their lives to do the right thing; Sully returns a favor by reaching out and saving his friend's life in Doc's hour of greatest need.

Tensions still run high in the Yokas household; Lester preps Bosco for Mikey's hearing, and then pulls a switch when he cross-examines him on the stand, leading to Mikey's getting RORd; Sully realizes what a toll the job has taken on him by his reaction to the deaths of three people in a robbery at the restaurant where he eats breakfast every day; Faith and Bosco answer a call which leads them to Lester's house, where they find his daughter not breathing; Sully tracks down and arrests the restaurant murderer; after Dr. Hickman tells Faith and Bosco that Lester's wife and daughter have been severely beaten, Lester is arrested; Sully gets his LSAT results; Ty and Sasha get closer.

In order to get enough evidence to convict C.T. Finney for the death of Ty Davis, Sr., Sully must look for the other officers involved with the incident, and also relive the events leading up to the murder.

Cruz and Santiago try to track down a gang member who murders witnesses to his murders. Grace finds her mother, who doesn't seem to welcoming.

An explosion in a building about to be demolished leaves men trapped inside, forcing the firefighters to make terrible choices; Fred's drinking problem escalates; Doc cancels his date with Brenda.

Faith, Bosco, Carlos and a wounded Doc find themselves trapped in an abandoned tunnel and unable to reach Central on their radios; the firefighters get into mischief during a long lull between calls; when the C.O. can't raise Bosco on the radio, Sully tries to cover for him.

Bobby's attempt to keep Paulie away from drugs ends tragically.

Bosco arrests a pedophile posing as a toy store Santa, and the grateful store owner returns the favor by helping Bosco and Sasha come to the aid of a man whose house is robbed of all his children's Christmas presents; after Sully and Ty save a young homeless girl from a fire, she rekindles Sully's Christmas spirit; Carlos receives the ultimate Christmas present when his brother arrives at the firehouse bearing the gift of being a perfect bone marrow match for Kylie, as well as the news of Carlos's real name and family history; Kim and Jimmy spend a romantic Christmas Eve together; Sasha's search for the perfect gift for her nephew gives Swersky the opportunity to play Santa.

Doc and Carlos are rescued by the firefighters when they get trapped in an eighteenth floor apartment with a patient who cannot walk; Ty comes to the end of his probationary period; Faith discovers that she's pregnant again; the firefighters come under fire from a madman when they arrive to fight a car fire.

Bobby comes to the aid of his old friend Paulie after Paulie's sister begs Bobby to help her brother with his drug addiction, but becomes enraged when Paulie breaks into Bobby's mother's house and robs her to support his habit.

After a despondent woman steps off an eight-story apartment building, the squad finds themselves in a race to transport both the woman's heart and a dying girl to a local hospital in time to save the youngster's life. The suicide hits home for Faith as she comes to grips with her own ongoing medical problems, while Doc expresses concern over the emotional effects this case will have on Kim, despite her constant reassurance that her accident was not an attempt to kill herself.

Even though his co-workers want to nominate him for the "Paramedic of the Year" award, a pensive Doc is disheartened as he considers his unfulfilled life. He later teams with Kim as they try to save a heart-attack victim while fending off a woman wielding a meat cleaver. In addition, Doc tries to minister to a chronic old drunk and a teenaged girl who attempts suicide in her bathtub. Meanwhile, Faith secretly undergoes a procedure to determine if the lump in her breast is cancerous, leaving an unsuspecting Bosco assigned to a nervous rookie cop; Kim reluctantly consults a lawyer about Jimmy's intention to claim custody of Joey.