Amikor Ethan Burke FBI ügynök autóbalesete után magához tér Wayward Pinesban, elkezdi felfedezni az ártalmatlannak tűnő kisváros sötét titkait...

Miután Ethan megtalálja Bill Evans titkosügynök holttestét egy elhagyatott házban, Beverly segítségével további nyomok után kezd kutatni. Mindeközben Theresa és Ben úgy dönt, hogy Idahóba utazik Ethan után, aki megtudja, hogy Wayward Pines lakosai miért kötelesek felvenni a telefont.

Amikor Beverlyvel végeznek a főtéren, Ethant teljesen megdöbbenti, hogy Kate is részt vesz a barbár szertartáson. Bár elhatározza, hogy megtalálja a Wayward Pinesból kivezető utat, Peter találkozik Peter McCall ingatlanügynökkel, akitől kap egy új házat. Mindeközben Theresa és Ben Idahó felé tart, hogy megtalálják Ethant, aki újra összetűzésbe kerül Pope seriffel.

Harold's failed attempt to break past the fence surrounding Wayward Pines leads to questions from Ethan about other insurgents who have gone off the grid. Amy's health takes a turn for the worse. Nurse Pam pushes Theresa to investigate Plot 33. Ben is encouraged by his teacher to speak publicly about current events.

Trapped outside the fence at the end of the first episode, Xander returns to Wayward Pines - bringing someone unexpected back with him who helps him learn more about the Abbies' intentions. Meanwhile, Rebecca puts herself at odds with Megan in order to help Lucy, a young girl who is trying to escape a Wayward Pines tradition, and CJ leads a brave group on an expedition beyond the fence to expand humanity's claim on the Earth, despite Theo's protests.

Rebecca recalls first meeting Pilcher as an architect and the creation of Wayward Pines is revealed. Theo is shocked by a secret Rebecca divulges to him; Teresa tells CJ and Adam she wants to live outside the protected walls as Megan experiments on the first female Abbie that has been captured.

The Abbies attack CJ and the harvesters, leaving Teresa in grave danger and the town dangerously low on food supplies. Then, Theo constructs a makeshift triage unit, but he may not be able to repair his marriage to Rebecca. Also, Xander still has some fight left in him as Jason questions his abilities to lead.

Theo and Megan disagree over the Abbies' intelligence, as the doctor attempts to communicate with their leader. Then, an underestimation has deadly consequences. Also, CJ reflects on his life and the great responsibilities he's had over the centuries.

Theo teams up with Hassler to track the escaped Abbie leader; Xander confronts Rebecca about her condition and Jason learns devastating news about Kerry.