Thousands of abbies gather outside of Wayward Pines as the fence power cuts out.
David watches the monitors showing the abbes approaching.
As Theresa and Kate try to calm the townspeople, Ethan calls Pam at the complex. She says that the power is out across the town, including the fence, and that abbies are moving in. Ethan tells everyone to head to the Plot 33 bunker, while Theresa goes to the hospital to get Ben. Kate tells Tim to get all of the subversives together and arm themselves.
At the complex, Vince tracks the approaching abbies and Gina warns that they only have 20 minutes until power is restored.
The backup power comes on at the hospital and Ben tells Amy that she went into surgery. As he says that he didn't want to lose her, Theresa comes in and says that they have to leave immediately. Ben refuses to leave Amy behind and Theresa agrees, and they go to find Dr. Carol.
The wounded Jason wakes up in a cell at the sheriff's station. Ethan and the others come in and arm themselves, and Tim finds the pipe bombs that Franklin made.
Pam goes to David's office and he says that they need to prepare to awaken Group C. She warns that Group B will be killed, but her brother says that the town is too sick and they're already dying because he failed them. He figures that once the abbies migrate in the winter, they can start again. Pam says that there is still time to fix it, but David insists that they have to start again and take more direct responsibility. She says that she's followed David blindly for years, but they've gone too far. Now he has to just let his experiment go. Pam says to send the guards, and David calls in the guards... and has them put Pam in suspension.
Guards capture the surveillance techs and take them away as well. On the monitor screens, the abbies swarm the town.
Dr. Carol warns that Amy is too weak to move. He goes to check on the backup generator and Theresa nods to Ben.
At the sheriff's station, Ethan tells Kate that he'll meet her at the bunker. As they leave, Jason says that David warned them that the day of reckoning would one day come, and he would save the First Generation while everyone else died liked Harold. Kate considers shooting him but then goes with the other subversives, leaving the teenagers in their cells.
Dr. Carol tries to get the backup generator going, and an abbie finds and kills him.
David puts on some classical music and starts reading a book.
The abbies find the townspeople on the streets and start killing and eating them. At the hospital, Theresa hears abbies moving through the hallways and leads Ben and Amy out.
Kate and her people open fire on the abbies, while Big Bill hides in a lot. An abbie finds and kills him. Another one goes for Arlene but Kate shoots it dead and tells her to get to the bunker.
The guards lead Pam and the techs to the suspension cells. Pam tries to get through to one of the technicians, Christina, and reminds her and the guards that they all agreed to join David on his journey. There are more pregnancies in Wayward Pines than ever before, and their duty is to the First Generation, not to David. Pam says that they can still turn it around if they work together, and a guard tasers her unconscious. When one guard hesitates, the leader Robert tells him to shut up and orders the techs to put on their suspension suits.
Other First Generation members break into the sheriff's station and free Jason and the others. They debate what to do next and Jason says that they have to make it to the ark.
Kate's gun jams and she's forced to take shelter in the toy store workshop. An abbie chases her inside and she locks herself in the back room. Another abbie bursts through the skylight and Kate clubs it to death.
Theresa and Ben find a trail of blood and duck into a record room. When Theresa tries to shut the door, an abbie grabs her wrist. She grabs a syringe and jams it into the creature's eye, and Ethan arrives to shoot it dead.
Kate goes back out onto the street and finds an abbie eating Tim. He's still alive and points at the nearby pipe bombs. Kate grabs them and runs off while the abbie finishes feeding.
Ethan and the others drive to the bunker and get inside with the surviving townspeople. Kate arrives and gets inside, and Ethan seals the hatch. He asks Megan about the tunnels, and doesn't believe it when she denies knowing anything about it. Kate warns that everyone will die if she doesn't help them, and Megan insists that David will rescue them. Ben points out that David didn't warn them, and Megan finally says that the tunnel leads to an elevator which will take them to the complex and David. Ethan , Theresa, and Kate go to check it out and Ben turns away from Megan.
Ethan and the women find the tunnel and Kate shows him the remaining pipe bombs. Kate confirms that she has two magazines of ammo left, and Ethan goes back for the others. As Kate tends to Theresa's injuries, she offers her condolences on Harold's death. Kate admits that she really loved her husband.
Back with the others, Ethan shows Ben how to use a pistol. Ben apologizes for what he said earlier at the hospital, and Ethan assures Ben that he loves him and they'll get through what's happening. He then starts leading everyone to the tunnel. Megan tells Brad that there may be survivors and she's going to stay behind to let them in. Brad insists that no one outside is alive, but Megan insists that tells Brad to make sure the children get to the complex. After a moment, he kisses his wife on the forehead and goes after the others.
At the academy, Jason and the others find the other First Generation members waiting in the orientation room. He opens the door to a secret storage room with food and weapons to last them for decades.
Ethan leads the townspeople through the tunnels to the elevator. He and Kate go up and Ethan gives Theresa a radio so he can call her when they know it's safe.
The guards place Pam in a suspension chamber and David watches as they put her under. Once it's done, he walks away.
When the elevator reaches the complex, Ethan and Kate run out and shoot the guards. The guards in the suspension chamber hear the shots and in his office, David spots Ethan on the monitors. Meanwhile, the guard that protested earlier orders Christina to wake Pam up.
Ethan and Kate ambush the guards and order them to surrender. They're forced to shoot one of them and the rest get down on the floor. Ethan then radios to Theresa to start sending people up.
Megan hears the abbies pounding on the hatch and stares as they break through.
Ben goes back and starts shooting as the abbies charge down the hallway. Meanwhile, Theresa fills the elevator and waits for it to return. Arlene takes Amy with her, and Amy tells Ethan that Ben is down there and the abbies are inside. Ethan takes the pipe bombs and tells Kate to find David and make him turn on the power. He then gets back down just as Ben's gun jams, and opens fire on the abbies. The last group of townspeople gets into the elevator and Ethan closes the door just in time.
Partway up, the elevator stops and they realize that the abbies are climbing the shaft and have cut off the power. Ethan opens the roof hatch and sends Ben and the others up. Theresa is last, and Ethan makes her promise to stay close to Ben. He kisses his wife and hugs her, and helps her up. Ethan then tells Ben that he's right behind him, and says that they have to keep the abbies from coming up. Ben reluctantly goes, and he and the others climb up to the top doors. The other townspeople pry open the doors and get them up.
In the elevator, Ethan takes out the pipe bombs. David watches him on the elevator monitor and says that the abbies will climb up and kill everyone. Kate comes in and orders David to restore the power to the fence. He refuses, saying that he has sown the seeds for the future and his ideas will live on after him. David tells Kate to kill him, but before she can, Pam arrives and shoots him dead. The technicians rush to turn the power back on.
Ben climbs up and hugs Amy.
In the elevator, Ethan sits and watches the abbies break through the floor. He remembers celebrating Ben's birthday with Theresa, and then sets off the pipe bombs. The elevator crashes down the shaft, killing the abbies. Above, Ben and the others realize that Ethan has sacrificed himself. Debris comes shooting up and hits Ben in the head as he looks for his father.
Later, Kate finds Pam and tells her that Ben is still unconscious. Pam starts to get the food organized, and Kate says that she wants to help and she's better with more information. They go to the suspension chamber and Pam explains that it's the rest of the population that haven't woken up yet. Kate wonders if she's lying, and Pam says that there can't be any more surveillance or lies, because they have to survive because they're the last of humanity.
Three Years Later
Amy wakes Ben up. She's dressed as a nurse, and explains that he's in Wayward Pines and she's a nurse there now. Amy says that she graduated two months ago and keeps calling him Mr. Burke. When Ben wonders what's going on, Amy finally says that he's been unconscious for three years and warns that "they" are listening. She then whispers that after his accident, they put him into suspension after his accident along with the rest of the adults. The First Generation blamed Ethan for David's death and thought Ben was like his father. Amy convinced them that Ben was different, and he staggers out of bed and out of the hospital.
Ben walks down the street and discovers that things are back to normal. Jason is the new sheriff, and smirks at Ben. Families and their children are at the carousel, and there is a statue of David heralding him as a visionary. Adult corpses are hanging nearby.