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.

Theo teams up with Hassler to track the escaped Abbie leader; Xander confronts Rebecca about her condition and Jason learns devastating news about Kerry.

Pilcher recalls finding his Chosen One. Then, as the Abbies close in, Jason makes a fatal judgment call and Theo and Xander must put aside their differences to stop him before the human race is lost.