Secret Service agent Ethan Burke wakes up after a car accident and finds himself in the hospital of an isolated town named Wayward Pines. However, he soon discovers that time passes differently in the town, and that some familiar faces are not so familiar.

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. Elsewhere, Theresa and Ben decide to take their search to Idaho.

While Ethan confronts Kate after the Reckoning, Theresa and Ben get a lead on Ethan's location. Pope is on hand to greet them as they arrive in Wayward Pines.

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. Meanwhile, Ben receives private tutoring from Megan Fisher on his first day of school; and Theresa is offered a job as a real-estate agent.

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; and Megan Fisher teaches Ben the truth about where he's living.

Ethan gets a tour of the facility and personnel that manage the day-to-day operations of Wayward Pines and learns more about the history and how the residents ended up in the eerie town. Meanwhile, at the realty office, Theresa finds a map of an unusual plot of land she wants to investigate and Kate and Harold are planning a covert operation.

Ethan tries to tell Kate and Theresa the true about Wayward Pines, but they assume that the authorities have gotten to him. Meanwhile, Megan teaches the first generation about reproductive human biology, and Pam talks to Kate and Harold about their fertility issues.

After an explosion on Main Street leaves two key residents of Wayward Pines in critical condition, Ethan is determined to find out who is responsible for the horrific act. Meanwhile, Harold opts out of the covert operation he and Kate were planning, and Nurse Pam interviews surveillance engineers to find out if there are any workers responsible for falsely reporting activities of any Wayward Pines residents.

After Harold attempts to break past the fence surrounding Wayward Pines, Ethan interrogates him about other insurgents who have gone off the grid. Meanwhile, Amy's health takes a turn for the worse, Nurse Pam encourages Theresa to investigate Plot 33, Ben's teacher, Megan Fisher, advises Ben to speak publicly about the current events effecting Wayward Pines and Ethan reveals the truth about the town to the residents.

After Pilcher decides to turn off the electricity in Wayward Pines - with deadly repercussions - Ethan and Kate take the initiative to make sure everyone is out of harm's way. Meanwhile, Nurse Pam confronts Pilcher on his decision and tries to convince him to reconsider, Ethan and Kate plan for an attack and the first generation tries to protect the future of Wayward Pines by taking matters into their own hands.