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.

In a series of flashbacks, we learn how and why Jason Higgins was raised to be the leader of the first generation and favored child of Wayward Pines. Meanwhile, Nurse Pam 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.

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.

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.

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 and Megan disagree over the Abbies' intelligence, as the doctor attempts to communicate with their leader. Then, an underestimation has deadly consequences. Also, CJ reflects on his life and the great responsibilities he's had over the centuries.

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.

As the Abbies descend upon the town, Theo is forced to make a decision that could seal humanity's fate