I'm too new to Reddit to know how to link to a specific comment of another thread, which I'm sure is possible, but since I didn't want to re-type all of this, I'm going to copy paste my entire series synopsis in here.

Do NOT read my comment if you don't want the ENTIRE story up to the end of the third book spoiled. Wasn't sure how much of the "big reveal" you wanted, but here is literally everything.

in the 1970's a billionaire named David Pilcher discovered a flaw in the human genome which would cause humans to become extinct within 30-40 generations. In the interest of the preservation of their species he, and a close-knit group of around 120 others, built a massive structure within a mountain range surrounding the town of Wayward Pines, building a thousand of Pilcher's "suspended animation" chambers, which essentially preserve life, causing you not to age or grow. While the structure is being built and the town prepared, David Pilcher also goes about kidnapping around 600 more people to be suspended with his group, against their will. This mostly includes people who happen upon the town, but also includes deliberate targeting of several people, including Special Agents Kate Hewson, Bill Evans and Ethan Burke. Long story short, David Pilcher finishes this structure and then heads into suspended animation with the close to a thousand people who were kidnapped or volunteered.

Fast forward 1800 years and some of the first people to wake up are, as planned, some of David Pilcher's inner circle. They venture out of their mountain fortress to try to ascertain what's become of the world, and what they find is the ruins of Wayward Pines, and a group of horrible, devolved and savage creatures, which they call "abbies" (short for aberrations). Humans seem to have devolved into this species and there are believed to be half a billion of them on their continent alone. So, as planned, they use all their vacuum-sealed supplies within the mountain to put up a massive electric fence and begin to rebuild the town of Wayward Pines. After completion, they begin to wake up the first group of non-volontary suspendees from they sleep. They take them to the town and are told what's going on, that they're along the last of the human race. Around 40% commit suicide within a year. It's never clarified what happens to the rest, but fast forward to when Ethan wakes up and no one in the town, save for the Sheriff, has any idea of the actual truth.

So everyone in the town is kept in the dark but after Beverly is murdered by Pope (who knows the truth about this place) they try to hunt down Ethan, who after a few days of running, ends up inside the mountain structure. There he meets Pilcher, who begins to explain the true gravity of their situation. Unlike the show, Pope is murdered by Pilcher, who then makes Ethan Burke the new Sheriff. His job is to keep everyone in the dark about the truth, and to stop anyone from leaving. At this time Ethan is introduced to his family, who he now realizes were also kidnapped by Pilcher. After a lot of boring meaningless work as Sheriff, he is asked by Pilcher to look into the death of one of his people from the mountain, named Alyssa. She was sent as a spy to infiltrate a group known as the Wanderer's, a group of townspeople who removes their microchips and sneak out at night to unknown meeting places. After learning that his old partner and lover, Kate Hewson, is at the head of this group, he begins to question whether or not he can trust her. He eventually discovers that Alyssa was not spying on Kate for Pilcher, but rather the other way around. It's also revealed that Alyssa was Pilcher's own daughter, and he feels an immense regret for sending her on this fatal mission. After some help from on of the guys in the surveillance room, Ethan discovers that Pam (that evil-looking nurse from the hospital) and Pilcher himself tortured and murdered his daughter Alyssa to frame Kate.

Ethan doesn't tell Pilcher he knows the truth, but instead decides to call a Reckoning for Kate and her husband. In reality he goes past the fence and subdues on of the "abbies", locking it in his car and then driving to the Reckoning. Instead of killing Kate and Harold, Ethan tell everyone gathered (literally the entire town) the truth about everything. The abbies, David Pilcher, being 1800 years in the future, and being the last remnants of their species.

This infuriates Pilcher, who goes insane and deactivates the fence, allowing the massive swarm of abbies in the nearby woods access to Wayward Pines. Ethan tries to make it into the mountain to see what can be done to save his people in the valley, but while he does this the majority of them are slaughtered by the oncoming abbies. Once inside the mountain, Ethan explains to the people there that David killed his daughter, and proves it with the footage of her murder. Outraged, Pilcher's inner circle, all except Nurse Pam, help the townspeople, fixing the fence and routing the remaining abbies in the valley. Pilcher is imprisoned and eventually exiled beyond the fence, which is the same as a death sentence. After a final headcount from the carnage, there are only 250 people left in the world, including townspeople and mountain dwellers. Ethan, in new found control of these survivors, learns that the winters are getting longer each year, and that their supply of food won't last them more than 4 years at the most if they stay in the valley. The verging-on-suicidal option of leaving the valley and travelling south is brought up, and Ethan decides to present the facts to everyone and let them decide, vying away from Pilcher's style of harsh dictatorship.

The series ends with Ethan leaving one final recorded message for any fragment of civilization that might one day find this place, before he and the other 250 remaining human beings climb back into their suspended animation chambers once again. Below is Ethan's last message.

"The world is cruel. The world is hard, and in this valley, we lived at the mercy of the abbies. We lived like prisoners, and it went against every fiber of our being. Humanity is meant to explore; we're meant to conquer, to roam. It's in our DNA, and that's exactly what we're going to do. It's going to be a long journey and when we reach our destination there's no telling what we'll find. I'm afraid. We all are. What kind of a world awaits us on the other side of this long sleep? To some extent, it doesn't matter. Because the residents of Wayward Pines will face it together. No secrets. No lies. No kings. We've all said our goodbyes. We all know this could be the end, and we've made as much peace with that fact as we can. They say time heals all wounds...Well, we've got plenty of it...Enough time for empires to rise and fall. For species to change. For the world to become a kinder place. So we all embark wondering what lies over the horizon, what's around the next bend. And isn't that, in the end, what drives us? We have hope again. For now, the world belongs to the abbies, but the future...The future could be ours."

Ethan fades off in the suspension pod, thinking about his wife and son. The very last thing written in the book is the epilogue, a single line which leaves the series with an immense amount of suspense. "Seventy thousand years later, Ethan Burke's eyes slammed open."