Darwyn struggles to maintain his cover as he assumes command of a new Los Angeles sleeper cell and questions the experience and skill of his new FBI case agent. Farik's interrogators use new techniques to get him to talk.

Ordered by the terrorist network to acquire a powerful weapon, Darwyn finds the FBI unwilling to cooperate. Ilija faces a heartbreaking decision as he prepares to flee for Europe. Farik is expatriated to Saudi Arabia, where he can be tortured.

Darwyn risks blowing his cover to stop one of his cell's operative from taking revenge against a progressive Islamic televangelist; Farik escapes from prison in Saudi Arabia and finds an al-Qaeda safe house.

The future of Darwyn's cell is altered when he urges the FBI to intercept a shipment of nuclear material arriving at the Port of Los Angeles - sent by none other than Farik; Ilija faces his past when he arrives home in Sarajevo.

The cell's new leader, Karrar, pushes Darwyn aside as plans progress for the nuclear attack on Los Angeles; Farik teaches a lesson about the terrorist way of doing business to an American philanthropist at a school in Yemen.

The FBI and Darwyn move to intercept the cell's plans to detonate a pair of nuclear dirty bombs in Los Angeles on the Fourth of July, but their victory is overshadowed by a pair of tragedies for Darwyn.