Secret Service Agent Ethan Burke begins his investigation into the disappearance of two federal agents.

As the residents of Wayward Pines struggle against the rule of the First Generation, a new resident emerges from suspended animation to help preserve the endangered human race.

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.

In a series of flashbacks, we learn how and why Jason was raised to be the leader of the first generation and favored child of Wayward Pines. Meanwhile, Nurse Pam (guest star Melissa Leo)  resurfaces and becomes a lethal threat to the town, and Theo continues to dig deeper into why he was specifically chosen to be part of the population of Wayward Pines.

Xander returns to Wayward Pines with someone to help him learn more about the Abbies; Rebecca goes out of her way to help a girl trying to escape a town tradition; C.J. leads a group on an expedition.

Rebecca recalls first meeting Pilcher as an architect and the creation of Wayward Pines is revealed. Theo is shocked by a secret Rebecca divulges to him; Teresa tells CJ and Adam she wants to live outside the protected walls as Megan experiments on the first female Abbie that has been captured.