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.

President Martinez orders Director of National Intelligence, Blake Sterling, to root out the mole from their staff, which causes Sterling to question his judgment of people close to him. Sophia reasserts her power over Thomas and the other detainees, and she prepares them for the next leg of their mission. Elsewhere, with the aid of Madeline, Sean continues his hunt for answers, all the while trying to stay one step ahead of the covert agents who trail him.

Negotiations for the release of the Sleepers begin after Sophia triggers a national disaster; Sean and Vicky continue their mission.