The first season of this psychological thriller based on a trilogy of novels by Blake Crouch and executive produced by M. Night Shyamalan begins with U.S. Secret Service agent Ethan Burke awakening from a car accident trapped in the seemingly idyllic, but secretly insidious, town of Wayward Pines, Idaho. It soon becomes clear that this peculiar Northwest hamlet is quite literally impossible to leave. The phones don't make outgoing calls, it's surrounded by an electric fence and the residents are under constant camera surveillance. Nobody is supposed to talk about the past or question the present. And anyone who tries to escape is punished via a public execution called a reckoning. With a history of mental illness and hallucinations, Ethan begins to question his own sanity as he investigates this tight-knit community, which includes fellow agent and former lover Kate Hewson, who has developed the façade of a Stepford spouse in order to ensure her survival. Before long, Ethan is reunited with his wife Theresa and son Ben, but now they too are stuck in this place where nothing is as it seems and no one can be trusted.
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. Elsewhere, Theresa and Ben decide to take their search to Idaho.
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. Elsewhere, Theresa and Ben head to Idaho.
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 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.
An explosion on Main Street leaves two key residents of Wayward Pines in critical condition. As Ethan works to determine who's responsible for this horrific act, Harold opts out of the covert operation he and Kate were planning. Meanwhile, Nurse Pam questions surveillance engineers to make sure no workers are making false reports.
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; and Ben is encouraged by his teacher to speak publicly about current events.
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.