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.
The Abbies develop a new tactic to try and get through the fence, and Jason is forced to send harvesters out to gather vital crops from a field beyond the barrier. Meanwhile, Theo realizes that the powers that be can't do without him and begins to assert his authority.
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.
One of the original townspeople returns from a scouting mission, and helps Theresa look for a missing Ben. Meanwhile, Rebecca crosses swords with Megan over the latter's intention to have Lucy breed children.
Rebecca's past with Pilcher is revealed. In the present, Megan experiments with the first female Abby that they've captured, while Xander tells Rebecca to tell Theo the truth about the two of them.
Almost three dozen townspeople are killed trying to salvage the crops, and Theo warns Jason that they are critically low on medical supplies. Meanwhile, both Adam and Theresa are injured in the attack, and Rebecca continues to see Xander.
As the Abbies gather outside the fence, Theo desperately tries to establish communications with Margaret. In the past, CJ awakens every 20 years to check the hibernation facilities... and slowly comes to grips with the fact that the world that he knew is gone.
Jason and his soldiers launch a search for the escaped Margaret, and Wayward Pines begins to come apart at the seams from pressures both within and without.
Jason learns that only half of the sleep pods work, and he will have to choose who will continue on to maintain the future of Wayward Pines. In the past, Pilcher is forced to choose an alternative when the baby he selects to become the future leader of Wayward Pines dies unexpectedly.
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