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.

After finding Secret Service agent Bill Evans’ body in an abandoned house, Ethan continues to search for clues with the help of Beverly. Meanwhile, Theresa and Ben decide to go to Idaho to look for Ethan and Ethan finds out why residents of Wayward Pines always have to answer their phones.

Following Beverly’s “reckoning” in the town square, Ethan is shocked by Kate’s participation in the heinous act. Although determined to find his way out of Wayward Pines, Peter meets real estate agent Peter McCall, who gives him a new house. Meanwhile, Theresa and Ben head to Idaho to find Ethan, who has another run-in with Sheriff Pope.

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 is shocked by what he discovers. Meanwhile, Theresa reports to her new realty job and meets her first client who is as confused as Theresa about the eerie town and Ben goes through orientation and learns the truth about Wayward Pines from his teacher Megan Fisher.

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.