Neville and Jason follow Roger Allenford through a moving Patriot train. They are now his security detail, and though Roger doesn't want Jason around, Neville insists Allenford help him out, as they're both harboring his secrets. The train rolls onward, towards the White House. At an unscheduled stop, Neville notices Deputy Secretary Victor Doyle in one of the first class cabins. He's accompanied by his wife... who is none other than Julia Neville! Shocked, Neville tries to keep his composure as he formulates a plan.
Charlie, Miles and Rachel descend on the Patriot compound. Miles figures they'll have to kill about 40 soldiers before they get to Aaron, Cynthia and possibly Porter. It's certain death, but they don't have a choice. But when they turn a corner, all the soldiers are passed out on the ground. The soldiers inside are out cold too. Charlie notices Aaron's boots inside Horn's office, and the group follows his tracks to the entrance to an earthen tunnel. Miles doesn't understand what's going on, but as the Patriots start to come to, he knows there's only one way out... and it's through the tunnel.
Horn orders the recovered soldiers to find Aaron and Cynthia. In the misty wilderness, one of Horn's top commanders suggests they wait out the fog before continuing their search. But Horn is shaking, and he says they need to find Aaron now. Though his followers aren't aware, the tumor inside of Horn's brain is metastasizing, and death is looming. A soldier approaches Horn with news: Aaron is hiding out in a nearby abandoned high school. The Patriots immediately close in on their target.
After traversing the tunnel, Charlie, Miles and Rachel search for Aaron in a mist-filled forest. Miles wonders what the Patriots are doing with such a tunnel. Rachel stops as the group ventures on; she needs to go back to Willoughby to save her dad. But Miles insists she stay with them. Aaron is the priority right now, and if Porter is dead, then he gave his life so they could protect Aaron. Suddenly, Patriot troops emerge from the brush and corner the group. Miles lifts his hands in defeat, but Monroe comes out of nowhere to slit the Patriots' throats. He's a hassle to deal with sometimes, but Miles knows his old friend is a necessary evil at this point.
In the library of an abandoned high school, Aaron wakes up in stupor, with Cynthia lying next to him unconscious. Her knife wound is gone, miraculously healed by what Aaron can only assume was himself. Suddenly, a little boy appears and scares the daylights out of Aaron. Where did he come from? The boy says he lives in the high school and saw Aaron walk into the library holding Cynthia. The boy helps Aaron get water and nurse Cynthia back to consciousness. When she comes to, Cynthia tells Aaron the little boy he's talking to isn't real.
Miles yells at Monroe for losing Aaron, but Monroe doesn't care. All Monroe wants is his son. Miles needs help; his wounded hand is badly infected, and he's having trouble swinging a sword. If Monroe ever hopes to see his son again, he's got to help Miles get Aaron back. In the other room, Rachel worries that their time is almost up. She tells Charlie she loves her, warning they may die in the next day or two. Charlie lets down her guard and returns the affirmation.
In a flashback to six years before the Blackout, Rachel watches as Miles goes off to war. He tells her they have to stop. She should start a family with Ben because he doesn't love her. Unable to believe him, Rachel promises to wait for Miles to come back; they can figure this out together. All Miles has to do is tell Rachel he loves her. Miles apologizes and heads into the terminal.
Spying Neville on the train, Julia follows him into a luggage room, where they consummate their reunion. Afterwards, Julia explains that she left Atlanta right before the bombs fell. In the aftermath, she remarried in an act of self-preservation. Tom tells Julia he's on his way to kill the president to avenge her death. Julia tells Neville it's time for a change of plans: she'll stay married to Doyle; he'll keep his job. Everything they ever wanted is still within reach...
Cynthia tells Aaron he needs to confront the child in his mind, so he speaks with the boy as she watches from a distance. The boy says he represents the nanites; they know Aaron's "thinks," and he made them when he "woke them up," the night the bombs dropped. The nanites act out Aaron's thoughts for him, in hopes of helping him. In hopes of stopping the burning and killing, Aaron asks the boy to leave and take the nanites with him. Just then, they hear noises outside, and the boy calmly announces the Patriots have arrived.
Miles, Monroe, Rachel and Charlie enter the high school just before the Patriots. Miles has to hide out in a classroom, having become so weak he can barely stand up. Before passing out, Miles tells Rachel he loves her. In the gym, Charlie and Monroe engage in a firefight with Patriot soldiers. Aaron and Cynthia run for safety, but are stopped by a desperate Dr. Horn. He demands Aaron remove the tumor from his brain, but Aaron says he can't! Dr. Horn gives him a choice: remove the tumor, or Cynthia dies. As Aaron pleads, Dr. Horn shoots Cynthia in the chest and kills her.
In a fit of rage, Aaron tells the little boy to kill Horn... and kill all the Patriots. In the aftermath of the immolation, the boy asks why Aaron didn't just ask him to save Cynthia in the first place. Aaron realizes he allowed himself to succumb to anger first, but now he desperately wants the boy to heal Cynthia. The boy says, "I'm leaving, like you wanted," and disappears, leaving Aaron alone.