When his girlfriend Leila goes missing during a Caribbean cruise, Sean Walker accidentally uncovers a national conspiracy. Meanwhile, President Elias Martinez decides to release a group of detainees, much to the chagrin of Blake Sterling, the Director of National Intelligence.
President Martinez's staff must work diligently to evaluate the situation led in the aftermath of the plane. Meanwhile, Blake Sterling interrogates Sophia, the conspiracy theories expand, and a shady character reveals knowledge of the detainees' plans.
When President Martinez reveals a tough new strategy to force Sophia to reveal the detainees' plans, a new detainee, Maya, is thrown into the chaos. Meanwhile, Vicky and Carter are in possession of a very important hostage, and FBI Agent Collier's suspicions become more severe.
The White House grapples with a mysterious biological threat. Their only hope is to crack Sophia during interrogation. Meanwhile, Vicky and Carter keep their hostage captive while they await further instructions. FBI Agent Collier on her search for Leila, stumbles upon Vicky's secret life. Elsewhere, a powerful businessman, Dempsey with classified intelligence and ties to the White House, emerges from the shadows.
The biological threat intensifies The CDC rushes to identify the contagion and treat the infected people, while the White House and Director of National Intelligence face a difficult dilemma in their negotiation with Thomas. Meanwhile, Simon appeals to Sophia to turn on Thomas. Elsewhere, FBI Agent Collier closes in on Vicky and Carter, but appearances are not always what they seem.
President Martinez and the Director of National Intelligence, Blake Sterling fulfill their agreement with Thomas, but after their plan goes awry, they suspect that there is a possible mole in their midst. Elsewhere, Sean Walker digs for answers at Leila's home, where he encounters Madeline, a mysterious conspiracy theorist. Meanwhile, Simon's past is illuminated, and his allegiances are tested.
While Sophia and Thomas prepare for the next step on their mission, Sterling begins to see conspirators everywhere, including among his own people. Meanwhile, Sean and Madeline seek answers behind Leila's abduction and Michael's coercion.
While Martinez interrogates Michael personally, Vicky's superiors send her on a new mission.
Sophia sets a trap after discovering dissension among her people; Leila and Sean investigate Samantha's kidnapping and try to evade Dempsey.
President Martinez confronts the traitor in his administration, only to be met with threats of exposing the cover-up of Avias Air 514. Even after testing the loyalty of Isabel and Thomas, Sophia still suspects their subterfuge, so she sends Simon on a fact-finding mission. Her suspicions are confirmed when Thomas unveils a shocking new plan. Meanwhile, on the hunt for Samantha, Sean and Leila battle the mercenaries sent by Dempsey.
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.
Sterling and Richard rally to help President Martinez take control of the political fallout from the detainees' escape from Inostranka. Meanwhile, Michael joins the hunt for Thomas while leaving Leila in the keeping of an old friend, Diane Geller.
Thomas summons Sophia, Diane Geller, and the other Sleepers to reveal the contents of the game-changing message he received. With newfound intensity, President Martinez confronts Vice President Ray Jarvis about his betrayal. Sean blackmails Vicky into helping him on a mission of vengeance.
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 mourn their losses after negotiations are derailed; Sterling tries to test Simon's loyalties; President Martinez asks Sen. Lewis to find any remaining moles in the White House.
Vice President Jarvis agrees to meet with an adversary; Sen. Lewis reports the results of the staff blood tests; Sophia continues her search for the super weapon; Leila questions her place; Sean and Vicky find who they've been looking for.
The White House is rocked by the sudden illness of one of their own, leaving Chief of Staff Peel and Sterling to investigate possible conspirators. Michael Buchanan comes to the aid of Leila, but it leaves them both at risk of Sophia's wrath.
While Sterling and Chief of Staff Peel try to identify the traitor within the White House, Sophia continues her campaign. Meanwhile, Leila and Michael rescue Simon, and Sean and Vicky try to track down the courier transporting the sleeper weapon.
Sterling is forced to turn to Simon for help when they need an antidote for a fallen leader, unaware that Jarvis is scheming to stop them. Meanwhile, Sean and Vicky try to stop the death of thousands, while Sophia uses Leila to fulfill her goal of mankind's extermination.
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.
The White House is gripped by a power struggle of historic proportions, pitting Martinez and Chief of Staff Peel against Jarvis and his secret ally, Sophia. Elsewhere, Sean, Vicky, Sterling, and Simon race to stop the dispersion points for the virus.