Secret Service Agent Ethan Burke begins his investigation into the disappearance of two federal agents.
After finding Secret Service agent Bill Evans' body in an abandoned house, Ethan continues to search for clues with the help of Beverly.
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 fights his new role in the city and keeps looking for a way out especially after his family has arrived and wants to keep them safe.
Ethan goes through the forest and manages to cross the fence line where he discovers some truths about Wayward.
Ethan is taken to a secret structure in the city, where he discovers the rest of the truth about Wayward Pines. Meanwhile, Teresa does research on her own.
Grieved by the truth, Ethan decides to trust Theresa and tell her everything he knows. A group of insurgents are a threat to the survival of the population.
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.
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.
Pam confronts Pilcher, while Megan changes her mind and helps Ethan lead the townspeople to safety and the truth.
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.
Theo discovers the truth and his purpose for being at Wayward Pines. CJ launches a vital and life-threatening project off the fence.
Nurse Pam reappears as a lethal threat to the city; Jason's past is revealed.
Xander returns to Wayward Pines with an unexpected guest; CJ leads a brave group on an expedition beyond the fence.
Wayward Pines Creation Revealed; Megan experiments with the first woman; Abby and Frank struggle with their personal problems.
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.
CJ reflects on her life and the great responsibilities she has had for so many years; Theo and Megan disagree on the intelligence of the Abbies.
Jason and his soldiers organize a quest to capture Margaret and Wayward Pines begins to rid himself of the cracks created by pressures from both within and without.
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.
Theo is forced to make a decision that could seal the fate of humanity.
