We pick up three years after the events of season 1, with the first generation in power.
In a flashback, Sheriff Pope recruits Dr. Theo Yedlin for Wayward Pines. We see him wake up in the present.
They want him at the hospital to operate on a patient, but he makes a run for it. He gets caught again and they take him to the hospital. He's told he's the only doctor in the entire town.
Jason tells him a story about a government project and ask him to focus on the patient, who turns out to be Kate.
Ben leads a group of rebels who want to change things.
Arlene is shown being shocked in the hospital.
Kate wonders why Jason saved her. He wants to know where Ben and the rebels are.
Jason makes a speech asking the rebels to come forward and re-join the town.
Theo watches people being reckoned. Ben turns himself in to stop it.
Theo is finally reunited with his wife.
Megan tells Kate the rebellion is over.
Kate slits her own throat.
Theo is driven outside of the fence as the abbies attack the car and the wall.