Dr. Theo Yedlin wakes up after a night of drinking and finds himself in the town of Wayward Pines. Gunfire echoes in the sheet and the town's leader, Jason Higgins, tells Theo that the town is a secret government project to explore wartime trauma on civilians. But Theo soon realizes that something far more sinister is going on.

In the past, Jason is raised to become the leader of Wayward Pines if anything happens to David Pilcher. In the present, Jason is surprised when one of his mentors asks for his forgiveness, and to rejoin the community.