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.

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