Newly elected President Elias Martinez learns of the existence of a group of people detained in a secret government facility in Alaska, and plans to release them -- over the objections of his advisors. Meanwhile, Sean Walker plans to propose to his girlfriend Leila, but their Caribbean vacation is complicated by another couple who may have ulterior motives.
After surviving a plane crash in the middle of the Arizona desert, Sean learns the reason for Leila's abduction -- and ends up a murder suspect as he continues his search for her. President Martinez is briefed on the detainees and their remarkable nature, and intelligence director Sterling's conviction that they have a hidden agenda.
Sean breaks into an F.B.I. field office to try and find a lead on the woman he believes has Leila. When Sophia proves less than cooperative, Martinez offers amnesty to any of the detainees who will help find those responsible for what happened to the plane's passengers -- and finds a man willing to sell out his people.
After the F.B.I. massacre Sean convinces Agent Collier to help him find "Vicki," who is holding Leila hostage. Survivors of the Miama flight (including Leila's father) are questioned by Mr. Sterling and the government, and Thomas contacts the President demanding that Sophia and the other detainees be released.
The plane survivors begin to suffer from a deadly infection as Thomas tries to force the President to release Sophia and the others. Sean makes contact with Leila, but neither knows that he is being led into a trap.
Sophia is released so that the government can track her back to Thomas, and Simon risks his F.B.I. cover by acting to throw them off her trail. Sean and Leila are reunited, but must still find the rest of her family and clear him of a federal murder charge.
Agent Lee's cover is blown, prompting Blake Sterling to recall the day he learned that his own wife was a Russian informant. Sophie confronts Thomas and tries to reassert her leadership, and a conspiracy theorist leads Leila and Sean to a man who might be able to help them find her family.
After President Martinez interviews Michael Buchanan he begins to suspect that his Vice President was in on the assassination attempt. Sean is shot, and Leila kidnaps an ER doctor to try and help him.
Sophia learns that many of her people living out in the world do not want to go home, and Thomas plots to seize leadership from her. Sean and Leila find a little girl who may be able to lead them to Samantha.
Sean and Leila investigate a psychiatric hospital where they believe her sister is being held. Sophia suspects that Thomas is no longer under her control, and President Martizez's government discovers a nuclear missile preparing to launch against the United States -- under Thomas's command.
The government receives intelligence that more of Thomas' people are coming, and and a newcomer to the Senate suspects the President's involvement in a cover-up related to Mount Inostranka. Sean and Leila rescue her sister, while her father Michael gives Sophia an ultimatum.
Thomas launches a sneak attack on the Inostranka facility in a bid to free the detainees and win himself an army, leading to a stand-off with Director Sterling. Leila's father offers her a difficult decision, and Senator Lewis threatens to expose the government's cover-up on national television.
Michael and Sophia go after Thomas after they learn of his actions at Inostranka, and learn that he is seeking fuel to power a portal for his people. When President Martinez learns that Thomas is planning to steal uranium and cause a nuclear meltdown, he grows increasingly frustrated over his powerlessness.
Thomas receives a transmission from home, which forces him to change his plans and call upon Sophia. Vice President Jarvis returns to work, and Sean blackmails Vicky to help to track down Dr. James Dempsey, the head of the group that employed her.
After President Martinez has her people surrounded and gives Sophia an ultimatum, she pushes back with a very public show of power. Sean and Vicky head to the mountains of France in the hopes of finding Dr. Dempsey, who has made an archaeological discovery.
Having discovered Agent Lee's identity, Martinez and Director Sterling try and use him to find the remaining Sleepers. The President turns to Senator Lewis to conduct covert DNA tests to locate other moles, and Sophia makes a critical decision in the wake of the President's horrific actions. Meanwhile, Sean and Vicky draw closer to Dempsey.
Sophia attempts to manipulate the Vice President to target President Martinez, in order to disrupt the government while her people search for a weapon. Senator Lewis suggests that someone close to Martinez may be a Sleeper, and Dempsey tells Sean that he has a greater part to play.
After Martinez is hospitalized Director Sterling suspect that Vice President Jarvis is responsible for his condition, and attempts to prevent him from ascending to the presidency. On a tip from Leila, Sean and Vicky target a Russian ship to head off Sophia's hunt for an advanced weapon.
Sterling and Simon join forces to deliver an antidote to the President, threatening to expose Jarvis's alliance with the enemy. Sean and Vicky rush to stop Sophia's people from testing their deadly virus by releasing it inside a shopping mall.
Sean and Vicky board a plane in the hope of catching a man who is smuggling a deadly virus into the United States. Michael is given an impossible task to show his loyalty to Sophia, and Director Sterling finds evidence to confront Jarvis.
On the verge of introducing a deadly virus into the general population, Sophia begins to have second thoughts about the scope of her plan. Sean and Vicky cross paths with Simon and Blake, and Vice President Jarvis is under pressure when the President begins to recover.
Sean, Blake, Simon and Vicky race to stop Sophia from unleashing her virus at an international airport. President Martinez attempts to warn Jarvis of her plan and to regain his office, and the array is activated.
