President Martinez and his longtime Chief of Staff charge the intelligence community with decrypting Thomas's satellite message, but more importantly determining to whom it was sent. While they are distracted, Thomas unveils a surprise attack, but he does not anticipate a heroic stand-off with Blake Sterling, who learns an important lesson about Sleepers from Maya.
Meanwhile, newly appointed Alaskan Senator Catherine Lewis threatens to divulge information about the Mt. Inostranka detention facility on an episode of "HARDBALL with Chris Matthews." Elsewhere, Sean and Leila get a fresh lead on the whereabouts of Samantha, but it leads them to a dramatic turn in their lives. James Dempsey foresees that he and Sean will once again cross paths.
Still reeling from the attack in Alaska, President Martinez reasserts control over the situation and his administration, counseled by Sterling and his Chief of Staff. Sophia learns the details of Thomas's murderous rampage. Thomas sets Sophia and Martinez further at odds. Elsewhere, Michael leaves Leila in safekeeping with a close friend, Diane Geller, while he goes on the hunt for Thomas. The NSA continues to decrypt the satellite transmission, hopefully before it's too late.
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. Elsewhere, Dempsey continues on his hunt for experimental subjects.
President Martinez and Blake Sterling have the Sleepers surrounded, but after Sophia triggers a national disaster, negotiations ensue. Elsewhere, with a lead on the whereabouts of Dempsey, Sean and Vicky continue on their mission.
Sophia and the other Sleepers mourn their losses after negotiations are derailed. While observing Simon's reaction to the events, Sterling begins to doubt his loyalties and devises a test. President Martinez tasks Senator Catherine Lewis with rooting out any other moles within the White House. Elsewhere, Sean and Vicky are on the verge of tracking down Dempsey, but it may be exactly what he was anticipating.
Vice President Jarvis vocalizes his lack of faith in President Martinez's leadership and agrees to meet with an adversary. Senator Catherine Lewis reports the findings of her surreptitious blood testing of the White House staff only to find one holdout, someone very close to the President. Sophia pushes forward in her search for a super weapon. And, after witnessing injustices within the Sleeper community, Leila begins to question where she belongs. Elsewhere, Sean and Vicky find whom they've been hunting for, but it may be too late.
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. Across the globe in Russia, Sean and Vicky race to stop Sophia's weapon from being loaded onto a plane heading to the United States.
The White House grapples with the unfolding tragedy as Sterling continues the investigation into his primary suspect. Sophia manipulates the traitor inside the White House, confirming the suspicions of Chief of Staff Peel. Leila and Michael attempt to rescue Simon, but at tremendous personal risk. Elsewhere, Sean and Vicky try to identify Sophia's secret courier before it's too late.
Lee tries to get help taking the antidote to president Martinez. Sean and Vicky try to stop Sophia's virus at all cost and save hundreds of people. Jarvis continues as a puppet in the hands of Sophia... but something he wasn't expecting happens.