Rachel, Charlie and Miles have no choice but to enter the bunker to rescue Aaron, Cynthia and Gene. They plan to head to an access ladder on the roof but on the way they find all of the Patriots lying on the ground. Rachel asks if they are dead but Miles says they are out cold. The front door has been left open so they head inside. There are more men knocked out inside and Charlie finds Aaron's footprints. Miles wonders what's going on if Aaron was the one who knocked all of the men out. They follow the prints to an escape tunnel and go through it when the Patriots start to wake up.
Tom insists that Jason come with him on Roger's security detail. Roger points out that Jason escaped a training facility but Tom doesn't think that should matter. He helped Roger out so he agrees to let Jason come along. Tom tells Jason to smile because they are going to the White House.
Horn prepares his drugs when a soldier walks into his room. The man says that it looks like Aaron just walked away with Cynthia. Horn says there is no end to the surprises from Aaron.
Rachel, Miles and Charlie exit the tunnel on the other side of the town walls. The weather is strange and Miles asks if this is also the work of Aaron. Rachel wants to go back for Gene but Miles says they need to find Aaron first. She worries that Gene is dead and Aaron says that if he is, he did it to save them. They take cover when the Patriots ride by.
Aaron wakes up at the Willoughby High School. He rushes over to Cynthia and finds her pulse. She's still alive and her wound has healed. Aaron wonders if he was the one who did it. He hears foot steps run by and stands to look for whoever it was. A young boy asks him what he's doing here in his home. Aaron asks the boy if he saw who brought them there. The boy states that Aaron walked in carrying Cynthia but he doesn't remember that.
Charlie loses Aaron's trail but they find three Patriots walking through the mist. They are quickly taken out but a shot is fired that alerts more Patriots. Monroe rushes up and kills them from behind.
On a train, Roger asks Jason where Tom is. Jason says he went up front to see why the train is stopping. As Roger makes his way through the train, he looks out the window. He spots Julia with another man.
Aaron takes care of Cynthia and tells the boy that he hopes she will be okay. He asks the boy questions about himself. A Patriot stares in one of the windows at them.
Horn is in so much pain that he has trouble concentrating. He tells a soldier to ask Truman to send everyone he has. Horn needs to find Aaron and says he is almost out of time.
Monroe doesn't want to go help Aaron, he only wants to know where his son is. Miles shows Monroe his infected arm and admits he is having trouble swinging a sword. Monroe says Aaron isn't worth saving but Miles disagrees. If Monroe doesn't help, Miles promises to never say where his son is. Charlie tries to assure Rachel that they will rescue Gene. There is so much she wants to talk to him about and she tells Charlie that she loves her. Monroe agrees to help them look for Aaron. Rachel has a flash back to six years before the black out when she met with Miles before he left. He says he can't keep having an affair with her because she's married to her brother. Miles thinks she will be better off with Ben. She offers to leave Ben and wait for Miles but he doesn't love her. Rachel doesn't believe him but he has to go.
Horn sits in a wagon and notices some fireflies. The soldier who spotted Aaron in the school informs Horn of his discovery.
On the train, Tom approaches Julia. She notices him but he walks right by. She excuses herself and follows Tom to a luggage room. The two stare at each other before kissing.
Monroe thinks it's too quiet outside and Rachel worries that the Patriots are gone because they found Aaron.
Cynthia wakes up and the boy asks Aaron to talk. She asks who he's talking to because she doesn't see the child. The boy says "We fixed her and brought you back to life, and we want to talk." He leaves the room and explains what he saw to Cynthia. She suggests that he go talk to the boy and promises to be right there with him.
While putting their clothes back on, Tom asks Julia what happened. She headed south when Atlanta started to fall so she missed the bombs fall. He asks about the man that she is with. Julia thought Tom was dead so she married another man to survive. He says that he was on his way to assassinating the president for her. Julia says she loves him and outlines a plan to still get everything they want.
Aaron meets with the boy and realizes that it is Kevin, a childhood friend. The boy knows everything because the nanotech is everywhere, even in his brain. Aaron asks how the nanotechnology came to be alive and the boy says that Aaron woke them up. He asks why the nano brought him to life and the boy says it's because Aaron created them. Aaron asks to be left alone but the child says that the Patriots are here.
On the train, Tom gives Julia a fake name and asks Jason to take her back to her husband. Jason is surprised to see his mother but follows Tom's plan. Julia thanks him and heads back to her seat.
Miles and the group arrives at the school after Horn has already entered. They sneak inside and split up in the hallways. A Patriot enters the room that Aaron and Cynthia are in but they run away. Monroe heads for an exit while Charlie hides inside a locker. Rachel searches a room with Miles, when he feels faint. He shows her his infected arm and she asks why he didn't tell her sooner. Rachel refuses to leave him this time. There is a knock at the door and Miles admits he never should have let her go. She shoots the men that enter the room and tries to wake Miles up.
Aaron and Cynthia run down a hallway when they are stopped by Horn, who's holding a gun. He would be happy to let them go as soon as Aaron heals the tumor in his brain. Horn will shoot Cynthia if Aaron refuses to help. Charlie exits the locker and is immediately surrounded by Patriots. Monroe returns at this moment and kills the men. Aaron tries to call the boy to him while Horn counts down from 3. Cynthia says I love you to Aaron right before Horn shoots her. Aaron kneels over her body and looks up to see the child. He asks where the child was and he says that Aaron told him to go away. Aaron tells the boy to kill Horn and the rest of the Patriots. All of the men set on fire and die. The boy asks why he didn't ask to heal Cynthia. Aaron asks him to heal her but the boy is confused by his decisions. The child says he will leave now, like Aaron wanted.