In the aftermath of Flight 514's disappearance, Martinez demands answers from his staff and from Gloria. More is revealed of Leila's abduction and Michael's coercion. And the secret of the detainees is revealed... and the fact that some of their people are still at large.
When Sophia won't tell President Martinez what her people are up to, he offers a pardon to any detainees who tell him their plan. Meanwhile, Sean convinces Agent Collier that he's telling the truth, but at a painful cost.
Sean and Collier go on the run and try to track down Vicky. Meanwhile, Vicky and Carter prepare to kill Leila, Martinez appeals to Sophia for information after Thomas contacts him, and a mysterious affliction strikes the resurrected passengers.
As the passengers die of the contagion, Thomas delivers his ultimatum but President Martinez responds with a threat of his own. When Sophia realizes that Thomas won't back down, she sends Simon to relay her orders for Thomas to surrender the antidote. Meanwhile, Sean and Collier find Leila, and one of the government conspirators makes a fateful decision.
Sterling continues the operation to follow Sophia to Thomas, but discovers that a traitor within his organization is sabotaging his efforts. Meanwhile, Leigh and Sean go to the Buchanan house to search for clues to the conspiracy and meet an ex-journalist, and Simon finds himself running out of options when he must choose between the detainees and the FBI.
Blake closes in on the mole within his operation, while remembering the last time that someone betrayed him. Meanwhile, Sophia and Thomas prepare for the next step in their plan to return to their homeworld, and Sean and Leila rely on Madeline and her ally to find information on the missing Samantha.
Martinez's interrogation of Michael reveals the identity of the traitor within the President's team. Meanwhile, Sean is wounded and Leila abducts a doctor to treat him, and Dempsey gives Vicky a new mission.
Thomas and his lover plan to assassinate Sophia so he can take her place. Meanwhile, Sean and Leila try to track one of the escaped children, who may have knowledge of Samantha's location.
When Martrinez threatens Jarvis to force him to reveal the name of his conspirator, Jarvis threatens to go public with Martinez's cover-up of Inostranka. Meanwhile, Sean and Leila trace Samantha to a psychiatric hospital, and Thomas and Isabel reveal their master plan.
While the White House decodes Thomas' message transmitted into deep space, Thomas prepares to assault the Inostranka prison. Meanwhile, Sam and Leila locate Samantha, Michael escapes captivity, and a newly appointed Senator challenges Martinez on the Inostranka prison in her home state.
Thomas and his people secure Inostranka and prepare to free the prisoners. However, Sterling and a corporal manage to remain free and thwart their efforts. Meanwhile, Michael give an ultimatum to Leila, Sophia thanks Sean, and Senator Lewis confronts Martinez over his decision to illegally hold prisoners in her home state.
Martinez puts his people on high alert after Thomas' successful breakout of the Inostranka detainees. Meanwhile, Sophia and Michael learn of Thomas' plan to steal uranium fuel rods to fuel the power array and capture one of his people in an attempt to learn more, and Sean captures one of Dempsey's people.
Thomas receives word back from the homeworld in response to his message, and summons all of the sleepers together. Meanwhile, Sean convinces Vicky to help him track down Jarvis, and Martinez takes extreme steps to track down Sophia and Michael.
To protect her people, Sophia orders the destruction of a national landmark to force Martinez to withdraw his soldiers. Meanwhile, Sean and Vicky travel to France, where Dempsey has made a historic find.
The sleepers regroup after the death of their comrades, and Sophia forsakes her oath for the safety of her people. Meanwhile, Martinez launches a controversial program to test for sleepers and turns to Senator Lewis for help, only to discover a potential mole is closer than he suspected. In France, Vicky and Sean close in on Dempsey but are betrayed, and Simon must make a critical decision.
When Martinez and sterling reject Vice President Jarvis' input, he turns to an unlikely ally. Meanwhile, Senator Lewis reports the results of her blood test program to Martinez, and warns of a likely sleeper. Sophia and her people try to find the superweapon, while Dempsey confronts Sean and Vicky.
When Simon comes to Sterling with the counteragent for the President's "stroke," Jarvis sends Federal agents to stop them and keep Sophia from revealing his role in Martinez's illness. Meanwhile, Vicky and Sean try to stop the sleepers from using a mall to test their bioweapon, and Sophia seeks out a way to mutate the virus.
Martinez recovers and goes to confront the person responsible for putting him in the hospital. Meanwhile, Simon, Sterling, Vicky, and Sean finally team up to stop Sophia, unaware that she has already used Leila to develop a viable viral strain and is distributing it throughout the U.S.
As Martinez struggles to regain the Presidency, Sterling, Simon, Vicky, and Sean track down Sophia and Carlos at Dulles International and try to stop the release of the virus. Meanwhile, Peel organizes government forces to stop the sleepers at two other locations, Leila receives startling news, and earthquakes herald the true nature of the sleepers' arrival.