A Secret Service agent ends up questioning his own sanity as he searches for two missing colleagues in a strange town that he seemingly can't escape.

Ethan is helped by Beverly as he continues looking for clues to figure out how Secret Service agent Bill Evans' body ended up in an abandoned house; and he gets answers to the mystery of why people in Wayward Pines always have to answer their phones. Theresa and Ben decide to take their search to Idaho.

Ethan finds a bomb planted in his car, which leads him to question people he thought he could trust; Kate and Harold discuss their fertility issues with Nurse Pam; Ben's relationship with Amy heats up.

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.

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.

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.