Wayward Pines is torn in a conflict between the oppressive rule of the First Generation and a resistance group led by Ben Burke. Meanwhile, Dr. Theo Yedlin wakes up from suspension.
After being sent with Ben to the other side of the fence, Theo is brought back by Jason in order to operate on Kerry, while Ben is left on his own. CJ sets out on a dangerous mission to harvest the food on the other side.
Pam Pilcher, who returns with a deadly plan in mind, reveals the story of Jason, while Theo confronts his wife.
While on the other side, Xander stumbles on someone unexpected. CJ leads an expedition to look for fecund soil joined by Theresa, who makes a terrible discovery.
After capturing a female Abbie, Megan and her team conduct experiments on her. The story of Wayward Pines' inception becomes known. Hassler makes startling revelations.
Following the Abbies' attack on C.J.'s camp, Theo is forced to put up an ad hoc triage center; meanwhile, the food and drug supplies are running short.
CJ ruminates on his witnessing the gradual downfall of the human race and the unfortunate mutation it underwent. As Megan and Theo study the female Abbie, Margaret, Theo concludes that she's intelligent, whereas Megan disagrees.
Theo conveys to Kerry shocking news. When Margaret escapes, Hassler joins the force that went to hunt her down. After sneaking into Jason's office, Rebecca narrowly escapes death as Xander comes to her rescue.
With a deadly attack by the Abbies in the offing, Jason makes a fateful decision, with which Theo doesn't agree. As Pilcher looks back on a distant memory, a shocking truth is revealed.
As Jason's plan is set in motion, Theo comes up with a plan of his own in the hope of tipping the scales in favor of the humans in their battle against the Abbies.