I swear I wasn't entirely sober when I wrote this.
Wayward Pines Season 2 will take off from where Season 1 ended (which kinda took a page from a Boy's Love game if you ask me.) With the First Generation having taken over Wayward Pines post-Pilcher; a struggle to preserve the last of humanity is the premise of the season.
BUT how would you preserve humanity with about less than a hundred people remaining considering that Sheriff Higgins is a loose cannon on reckoning people; especially adults.
Since Pilcher is already gonna perverse the limits of science and technology anyway with longevity stuff; he also actually invested in Cloning Technology.
Ben Burke uncovers a secret journal which was locked deep in the Mountain Complex (a secret journal which is actually the one detailed in Sarah's Mntn_Pjt file) and when he reads its details; it says "Humanity is vanishing. Our only hope is to clone them..." (or something along those lines).
From the shadows; a hand grabs Ben by the neck. When the lights switch to the person behind Ben; it turns out that it's his father (or a guy played by Matt Dillon if you prefer).
Ben escapes and further discovered from a conspirator against the First Generation squad that cloning Ethan Burke was the secret pact between Pilcher and Adam Hassler.