Everyone in the 55th Precinct faces their worst fears when terrorists are discovered to possibly be building a dirty bomb. Carlos and Levine face trouble in their relationship. Captain Finney decides to end his life, rather than surrender himself for the murder of Ty Davis Sr. Brendan and Davis try to cover it up.

Cruz teams up with Rice to track down the terrorists associated with the possible dirty bomb.

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.

After a suspect in a jewelry store robbery starts displaying symptoms of a disease similar to SARS, the NIH is called in to figure out what is causing this, and hopefully stop this epidemic. Meanwhile, Cruz faces off with a gangbanger, who may have hired a 13 year old boy to carry out a murder.

The crossover continues on Medical Investigation S01E17 Half Life (II)

Cruz connects the dots that link Marcel Hollis to the murder of Darren Maddox, while Marcel begins to organize a street war against the 55th Precinct. Elsewhere, Yokas, Sully, and Bosco track a missing teen to a vampire cult.

Monroe and Bosco deal with an angry mother on welfare who shoots up the welfare office, Davis and Finney stake out a man and take down a prostitution ring, Faith deals with Emily, Cruz and Monroe recieve bad news about their health.

Faith investigates Bosco further, Sasha and Ty make up, Cruz goes for some spiritual healing, Carlos meets Holly's parents.

Finney and Davis are seriously injured in a car accident during a traffic jam, which was caused by a man trying to kill two people, and he succeeds. Emily's life is in danger when she falls in with the wrong crowd. Carlos buys an engagement ring for Holly.

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.

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.