Fox has yet to announce further details about "Wayward Pines" Season 3 but as fans await, writer Blake Crouch might have let on a little secret, which may possibly be the new season's main plot.
The final episode of "Wayward Pines" Season 2 just aired last July 27,2016 and it left quite a few cliffhangers, which made fans more eager to see Season 3 happen already. The second season showed surgeon Dr. Theo Yedlin caught in a crossfire between Jason Higgins, leader of the First Generation, and Ben Burke, leader of the underground rebels. The last season left off with Higgins in a critical condition as Dr. Yedlin tries to save him, meanwhile sacrificing some characters to carry a virus in order to cause an epidemic within the Abbies. The season's final scene was an Abbie holding a human child.
With the second season's final scene, it has been speculated that "Wayward Pines" Season 3 will take place sometime after Season 2. As depicted in the last season, some of the main characters along with half of the remaining human population, went into cryo-suspension to save humanity. With this, it is most likely that new season will start off those characters waking up to a different time hoping their plan for an epidemic worked.
The author of the original novels, Blake Crouch has shed some light on the new third season's storyline when he was interviewed by Entertainment Weekly. He divulged that in "Wayward Pines" Season 3, the series will finally address one of its key plots, which was that the humans who survived through the cryo-suspension will have to face the challenges of time and evolution. With that said, fans are expecting that there will be a rise in the population of Abbies as human evolution can advance into an Abbie. Jason Patric, who plays Dr. Theo Yedlin also forewarned that a lot of the "Wayward Pines" characters are not going to survive.
The date for "Wayward Pines" Season 3 has not yet been decided but it was revealed that the third installment may be the final installment of the series. "Wayward Pines" premiered on Fox in May 2015 and ran for two seasons. It is a television series adaptation based on the 'Wayward Pines' novels by Blake Crouch.