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.

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.

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.

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

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

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.

The electricity in Wayward Pines is turned off with deadly repercussions. As Ethan and Kate take the necessary steps to move everyone out of harm's way, Nurse Pam confronts Pilcher on his decision and tries to convince him to reconsider.

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.

Ethan is appointed to a leadership role in Wayward Pines and his first act, according to Nurse Pam, should be to call a reckoning for Peter McCall for his treasonous act of graffiti on Main Street. Ben receives private tutoring from Megan Fisher on his first day of school. Theresa is offered a job as a real-estate agent.

David suspects a traitor inside the complex helping the insurgents, and orders Pam to question the technicians. Meanwhile, Ethan is determined to stop more terrorist attacks like the one that put Ben in the hospital.

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.

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.

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.

Ethan learns more about Wayward Pines and its residents. Theresa sets her sights on investigating an unusual plot of land. Kate and Harold plan a covert operation.

New evidence is uncovered by Ethan, who, while still in shock that Kate participated in Beverly's "reckoning" in the town square, has another run-in with Sheriff Pope and is given a new house by a real-estate agent. Theresa and Ben head to Idaho.

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.

Ethan ventures outside of Wayward Pines and his shocked by what he discovers. Theresa shows up to her first day of work and meets with a client who seems to share her feelings for the town. Megan Fisher teaches Ben the truth about where he's living.