Producer M. Night Shyamalan revealed during an interview with Deadline that he and novelist Blake Crouch, who wrote the "Wayward Pines" book trilogy, have discussed what they might do if "Wayward Pines" gets a second season. Unfortunately, he did not reveal what possible plot points the season could follow. 

The widespread speculation is that season 2 would follow the story of Ben Burke (Charlie Tahan) as he leads a revolution against the First Generation, led now by Jason (Tom Stevens). Showrunner Chad Hodge indicated this when talking about the season 1 finale and what may happen in the future. 

"Maybe he will be able to change things. Or, maybe this is the way things should be," Hodge told THR. "What Ben does and how he responds will be up to your imagination to decide. There is no official season 2 yet. No talks yet. Nothing to report on that front." 

However, a rumor is spreading across the Internet that Ben Burke is not the only possible main character in case Fox TV decides to green light a second season. According to Vine Report, there is a rumor that Adam Hassler (Tim Griffin) might be the focus instead. 

In season 1, Hassler was Ethan Burke's (Matt Dillon) boss at the Secret Service. Toward the end of the series, it was revealed that Hassler was also put to sleep and awoke to discover that the future is indeed populated by mutated humans and that Wayward Pines is the only human civilization left. 

The character then took a group of survivors outside of Wayward Pines to check the outside world. They got as far as San Francisco, which they discovered to be in ruins, before they were attacked by Abbies. It is hinted that Hassler may have survived and could be on his way back to Wayward Pines.

All of this is still speculation at this point as Fox TV has not yet officially renewed the show for another season.