A Secret Service agent goes to Wayward Pines, Idaho, in search of two federal agents who have gone missing in the bucolic town. He soon learns that he may never get out of Wayward Pines alive.
Ethan's reactions to the incident among the insurgents result in a polarized response in the city. Pilcher decides to take care of the matter, endangering the city and all its inhabitants.
After what happened with Beverly in the plaza Ethan is shocked by Kate's participation. Determined to find his way out Peter meets the realtor, Peter McCall, who gives him a new house. Meanwhile, Theresa and Ben travel to Idaho to find Ethan who has another run-in with Sheriff Pope.
Ethan investigates the insurgent group after they create chaos in the city. A meeting is called to distract and gather the people of the city.
Pilcher returns in search of his Chosen One. On the other hand, as the Abbies draw closer Jason makes a fatal decision and Theo and Xander must put their differences aside to stop him before the human race disappears.
The Abbies attack CJ and the Reapers, leaving Teresa in grave danger and the city with alarming levels of supplies. So Theo builds a makeshift evaluation unit, but she may not be able to fix her marriage to Rebecca. Additionally, Xander still has unfinished business concerning him when Jason questions his abilities to lead.
The residents of Wayward Pines fight against the oppressive government of the first generation. Dr. Theo Yedlin, a new resident of Wayward Pines, awakens from a coma and finds himself in the midst of this rebellion, as he tries to understand what Wayward Pines really is and thus help preserve the endangered human race.