As Secret Service agent Ethan Burke begins to investigate the disappearance of two fellow agents in the mysterious town of Wayward Pines, Idaho, he realizes that he is unable to leave.
After finding the body of Agent Evans, Ethan tries to uncover the mystery of his death. He tries to escape with Beverly, but Sheriff Pope teaches him an unforgettable lesson.
Ethan's wife Theresa and his son Ben continue to search for him, and Kate advises him to play along and stop resisting. As Ethan reunites with his family, he faces off with Sheriff Pope.
Ethan becomes the new town's sheriff and he convinces his wife to play along till he can uncover the truth. Ethan is forced to make a tough choice regarding "the reckoning" of realtor Peter McCall.
Ben discovers the shocking truth about Wayward Pines from principal Fisher. Dr. Pilcher explains to Ethan that Wayward Pines is humanity's last hope.
Dr. Pilcher explains the history of the town to Ethan and tells him that he's tasked to bring order to Wayward Pines, while other groups attempt to escape.
Kate believes that Ethan has been brainwashed, and Ethan makes a shocking discovery about her. Ethan races against the clock to stop a bomb from detonating.
As the explosion leaves two persons critically injured, Ethan tries to find out the remaining members of the plot. Harold and Alan make an escape attempt.
Ethan finds out that the remaining conspirators have gone off the grid. Jason Higgins attempts to reckon Kate but Ethan arrives just in time. Ethan reveals the truth to the whole town.
As the townspeople attempt to escape from the Abbies, Ethan makes the ultimate sacrifice. Theresa and Ben escape in the complex, and Ben makes a shocking discovery.