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.

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