FAQ

He didn't. That scene is a flashback, but viewers were left in the dark about that fact so as to make them think that it was happening contemporaneously with Ethan's adventures in Wayward Pines.

Pilcher had predicted the gradual devolution of homo sapiens into the creatures shown in the show in an intensity proportional to the rapid environmental changes caused by humanity itself. The devolution involved an inactive genetic change (that would later on get active), happening gradually, until it was in the vast majority of the population. No matter what humanity would have done when it started getting active (build fortresses, eradicate the creatures), every living human would be devolved eventually.

Pilcher had gathered all the town's population when the genetic change was still very rare, obviously tested their DNA to make sure they didn't have it and put them under suspended animation which prevented the genetic change as there weren't living in the rapidly changing environment as the rest of the world but in a stable, "frozen" state. He had programmed the suspended animation chambers of his and his team to terminate the biosuspension AFTER the environment they would breathe and live in had been turned to normal.

Others who were not chosen, and did not have the genetic mutation, would have been killed off. Typical 'survival of the fittest' scenario.