Harold's failed attempt to break past the fence surrounding Wayward Pines leads to questions from Ethan about other insurgents who have gone off the grid. Amy's health takes a turn for the worse. Nurse Pam pushes Theresa to investigate Plot 33. Ben is encouraged by his teacher to speak publicly about current events.

The electricity in Wayward Pines is turned off with deadly repercussions. As Ethan and Kate take the necessary steps to move everyone out of harm's way, Nurse Pam confronts Pilcher on his decision and tries to convince him to reconsider.

Dr. Theo Yedlin – a new resident of Wayward Pines – awakens from suspended animation and finds himself in the middle of this rebellion, as he tries to understand what Wayward Pines really is and help preserve the endangered human race. CJ Mitchum, an original resident of Wayward Pines and a historian for the town with extensive knowledge of its complex origins, is the only one who can provide a unique bridge between the current world of Wayward Pines and the previous world that humans inhabited. Megan Fisher, is in charge of the scientific research being conducted on the Abbies, and remains deeply involved in the development of the hearts and minds of the future of humanity—Wayward Pines’ “First Generation”.

As Theo fights to make sense of his new life in Wayward Pines, he recognizes his value as the only surgeon in town and uses it as leverage to get answers to the many questions he has about the status of his wife, Rebecca, and the truth about the town from First Generation leader Jason Higgins. CJ Mitchum, an original resident of Wayward Pines and a historian for the town with extensive knowledge of its complex origins, is the one person who can provide a unique bridge between the current world of Wayward Pines and the previous world that humans inhabited. Meanwhile, Megan Fisher heads up the research being conducted on the Abbies, Theresa frantically searches for her son, Ben, and CJ Mitchum spearheads a vital and potentially deadly project outside the fence.

Trapped outside the fence at the end of the first episode, Xander returns to Wayward Pines - bringing someone unexpected back with him who helps him learn more about the Abbies' intentions. Meanwhile, Rebecca puts herself at odds with Megan in order to help Lucy, a young girl who is trying to escape a Wayward Pines tradition, and CJ leads a brave group on an expedition beyond the fence to expand humanity's claim on the Earth, despite Theo's protests.

The Abbies attack CJ and the harvesters, leaving Teresa in grave danger and the town dangerously low on food supplies. Then, Theo constructs a makeshift triage unit, but he may not be able to repair his marriage to Rebecca. Also, Xander still has some fight left in him as Jason questions his abilities to lead.