A federal agent goes undercover in Los Angeles to try and infiltrate a group of Islamic terrorists. Darwyn al-hakim finds an Islamic extremist guy named Farik. Farik asks him the join Sleeper Cell's plan to attack Los Angeles.
Farik and Ilija receive a deadly biological anthrax shipment which they prepare to use for an attack in Los Angeles. Meanwhile, Darwyn and his cellmates stack out a shopping mall as a terrorist target. Also, Darwyn's FBI boss wants to know what happened to Bobby who has disappeared.
Farik discovers that the money supply coming in from Mexico to finance Youmud Din has ceased. So, Farik, Darwyn and Christian cross the border to Tijuana, Mexico, and try to find a way to straighten out their financial troubles.
Farik decides to send biochemical student Eddy Pangetsu on a flight to Vancouver. There he must drive a shipment of real anthrax across the Canadian border to Los Angeles.
The Cell members end up posing as Iraqi insurgents-in-training to infiltrate and take over a warehouse to make it the new base of operations for Youmid Din.
Darwyn tries to get close to chemical plant worker in the hopes of trying to acquire some of the company's product for the cell. Also, Tommy's estranged mother visits.
Farik attends a meeting with cell leaders in Las Vegas as they finalize their plans for a date for their possible attack. Meanwhile, an Afghani boy comes to the warehouse in the hopes of becoming a jihadist himself. Also after meeting with Bobby's cousin, Gayle wonders if Darwyn could be a terrorist.
The cell works out a deal with white supremacists so they can acquire a large amount of explosives. The LAPD then sets up a surveillance on Darwyn after Gayle contacts them, which endangers his cover and gets the FBI's attention.
The cell hijacks a truck in order to acquire it's contents - a deadly chemical to be used in their attack. The FBI holds off on stopping the cell in the hopes of getting more information on the other 2 cells operating in the U.S.
Judgement Day has arrived and Fariq isn't yet out of surprises. A surprise diversion proves effective in allowing the cell to escape their surveilance. A quick thinking Darwyn leaves a clue that will hopefully lead the FBI to the target location in time.
Darwyn is trying to start a new life with his family but ends up back in another LA sleeper cell. Farik refuses to give up any information despite interrogation, and Darwyn's female FBI handler is kidnapped and beheaded in the sudan by terrorists.
The cell establishes its base and tries to get a rocket launcher while Farik foils another attempt at getting him to cooperate.
Darwyn is ordered by a terrorist group to get a weapon, but the FBI doesn't want to cooperate. Ilija gets ready to run away to Europe. Farik is sent to Saudi Arabia where torture is allowed.
Darwyn risks blowing his cover to save an Islamic televangelist. Farik escapes from prison is Saudi Arabia and finds a place to hide with Al-Queda.
Darwyn notifies the FBI that nuclear material is supposed to be delivered to LA.
Darwyn has to work with the new cell leader who doesn't include him in planning the next attack.
The FBI and Darwyn decide to move in an intercept the cell in their plan to detonate the two dirty bombs in Los Angeles on July 4th. However, Darwyn soon faces a pair of tragedies he did not see coming.
Darwyn ends up blaming himself for the tragedies that just happened to him and decides it is time to confront Farik, by using the leader's wife as bait.
