It's been three months since Rachel, Aaron, Charlie and Miles tried to stop the bombs from hitting the East Coast. They weren't successful. Philadelphia and Atlanta are dead zones, pits of darkness marked by only a few pockets of desperate humanity. Somewhere in the Plains Nation, Charlie tries to enjoy the life she has left by sleeping with a random bartender. When he mentions he's seen Monroe, her demeanor abruptly darkens, and she sets out to find Monroe in an entertainment encampment called New Vegas, where he's making money as a bare-knuckled boxer. Charlie stalks Monroe from a distance, trying to dig up information on his whereabouts and routines. She gets a carny to lure Monroe out of his trailer in hopes of meeting "a girl," but as Monroe walks to the bar, Charlie tries to kill him with an arrow shot. At the same time, two men attack Monroe, knock him out and drag him into the woods. Charlie's arrow misses, and she's left wondering what the heck is going on...
In Savannah, Georgia, Neville and his son Jason desperately case through an endless refugee camp in search of Julia, Neville's wife and Jason's mom. Neville realizes they'll never find Julia because she never would have left Atlanta. She would've waited for her family until the end of time, and because of that, she's nothing but charred remains now. The thought crushes Neville's soul. He puts a gun to his head, but Jason talks him down. Suddenly, a commotion outside causes the two to leave their tent. A beautiful schooner is docking at harbor, and it's flying the old Stars and Stripes. Secretary Justine Allenford gives a speech on shore about how the United States government is back to help its people following the attack. In fact, the President is on his way to the White House as she speaks! Everyone is excited, everyone that is, except for Neville. He's convinced these people were behind the bombings - and if they were, he vows to seek vengeance for the death of his wife.
In Willoughby, Texas, a bloodied Miles burns down a shed, then visits Rachel, who's helping her father, Dr. Gene Porter, run a medical clinic out of his home. Miles' hand is badly cut, and he's in severe need of medical attention. Dr. Porter patches Miles up and warns him to stay away from Rachel. She's been compulsively trying to pin down Randall's motivations for the bombing, and despite her lack of success, she's finally healing emotionally; the last thing she needs is the wrong guy. Elsewhere in Willoughby, Aaron is comforted at home by his new girlfriend, Cynthia. She's optimistic about the future of the world - after all, the lights came on right before the bombings, if only for a second - but Aaron is more pessimistic. While trying to grab firewood, Aaron is enveloped in a sea of fireflies... and has an epiphany about the biological energy capabilities in nature.
Later on, as Miles prepares to leave town for good, Rachel all but begs him to stay. He can't though; bad things happen when those two are together. On his way out of town, Miles witnesses a family being attacked by menacing figures outside their farmhouse and swoops in to stop the assault. Meanwhile, Aaron goes to Rachel with his thoughts about the fireflies, but she tries to write it off as nothing. Aaron knows he's not crazy - things have been really weird ever since the bombs dropped, for them especially. Just as Rachel is about to rebut this comment, Miles walks into town with a corpse strapped to his horse. Miles tells the town's sheriff they're dealing with a war clan, and a large-scale attack on the townspeople is imminent. The sheriff rushes to call in reinforcements, as Miles realizes he can't walk away from his past as easily as he'd hoped.
Later that night, a war clan member attacks Cynthia in her home, and when Aaron rushes to save her, he is slashed through the chest with a machete. Rachel tries to save him with the help of her father, but Aaron's lost too much blood. He dies; everyone in the room is devastated. Outside, Miles fights off a group of bandits attacking another set of townsfolk. He saves their lives, but soon realizes he's far outnumbered. Miles and the sheriff are taken to the war clan's base, where they meet the tribe's leader, Titus Andover, another whole level of creepy. Whatever's about to go down is not good. Luckily, Charlie lurks in the woods just outside of camp.
Rachel and her father console a grieving Cynthia. She can't believe Aaron is gone. Suddenly, fireflies overheard temporarily mesmerize her; they're so enchanting and full of energy in a blacked out world. Inside, Aaron lies lifeless on the floor. And then suddenly, he GASPS.
Three months after The Tower, the Mathesons settle in the town of Willoughby, Texas, where all is not what it seems.