Learning that Neville and his wife fled Philadelphia, Monroe becomes infuriated to discover Jason is still alive. The onslaught of revelations - how long had Neville been lying to him? - leaves Monroe questioning everything and everyone. In a fit of fury, he shoots the messenger, Captain Burke, in the head. Elsewhere, a dying resistance fighter slumps into camp on horseback and delivers a note to Miles right before dying. Monroe's snuck his nuclear bomb over the border into Atlanta, and Miles thinks he's just crazy enough to set it off. Together with Charlie and Nora, Miles decides to head for Georgia to halt a potential nuclear holocaust. It will be Charlie's first time outside of the Monroe Republic...
Once over the border and into Georgia, Miles knows his group will have to disguise themselves as soldiers if they hope to pass through the city gates into Atlanta. At a troop outpost in the woods, the group finds a cabin full of dead Georgian troops. Monroe's guys already got to them, and they took their spare uniforms with them. Miles, Charlie and Nora will have to take the clothes off the dead soldiers' backs. As they're doing this, Miles sees a familiar knife on a nearby table. He flashes back seven years, when he gave a fellow soldier and protege, Alec, the very same knife, a Matheson family heirloom. Now, Alec seems to be on the other side - and leaving messages for his former mentor.
Rachel leads Aaron to her friend Jane's home, since she knows more about The Tower than anyone else. But Aaron gets nervous when the path to Jane's location is through uncharted, and ominous, territory. His suspicions are confirmed when the two get jumped by two Militiamen. Just as Rachel is about to be raped by one of Monroe's men, both soldiers suddenly turn red and short of breath. Their skin smolders to a crisp as they collapse to the ground, dead, terrifying Rachel and Aaron. Suddenly, Jane appears out of nowhere, with a blinking handheld device in her hand. Whatever just happened, she saved their lives.
Aaron wants to know what the hell happened, but Jane merely invites him and Rachel to her house for sandwiches, where Rachel's delighted to see Jane's wife, Beth after so long. Once alone, Rachel asks Jane to help turn on the power at The Tower and destroy the nanites. "Even though they're keeping your son alive?" Jane asks. When Rachel pulls out the capsule she cut out of Danny's corpse, Jane begins to weep. The nanites aren't just keeping the power off - they have other uses too. Because of the nanites, Jane's beloved wife Beth has been able to survive-stage four cancer for 16 years. If Rachel turns on the power, she'll short-circuit the nanites, killing Beth. Beth strongly "suggests" that Rachel drop the matter - now.
Disguised as soldiers, Charlie, Miles and Nora sneak into Atlanta. The group searches around Atlantic Station, Atlanta's most bustling commercial district, for the bomb. Miles has just located the nuke when Alec attacks him in an alley looking very angry. As he rains down punches on the older Miles, an arrow suddenly hits Alec in the chest, and Charlie rushes in to stop the violence. Alec breaks off the tail of the arrow and grabs the nuke before losing himself in the crowd. Miles and Charlie sprint after him. When Miles finds him, Alec grabs a cop's gun and takes him hostage. Miles tries to talk Alec down, but Alec shoots the cop and throws him and the gun in Miles' path before running away. As Miles attempts to revive the officer, Atlanta police descend on him, assuming Miles committed the murder of one of their own.
Nora and Charlie know they'll never find Alec - and the bomb - without Miles. Unfortunately, the Atlanta police have arrested him. Charlie plots Miles' escape, but as she's looking for a way into the jail, Alec sneaks up behind her and pushes her against the wall. Alec begins breaking down Charlie's will, ridiculing her for naively following Miles. He was once in her shoes, until he found out who Miles truly was; when Alec realizes Charlie is Rachel Matheson's daughter, he encourages her to find out what Miles did to her mother. Suddenly, a Monroe helicopter drops thousands of fliers from the sky, and Alec runs away. Picking up a flier, Charlie sees Monroe's warning of a "nuclear event."
Miles is taken to see the Georgia Federation's President Kelly Foster at the top of a massive Atlanta skyscraper. She's received word that Monroe intends to detonate a nuclear bomb unless she surrenders by midnight. Miles pleads for his release so he can stop the detonation, but President Foster is still harboring ill will towards Miles for past bad blood - both personal and professional. Miles assures her if she doesn't let him stop Alec and Monroe's bomb, they'll be in the same dust cloud anyway. It's anyone's guess how Miles wins his release. Later that night as sirens wail, Miles meets up with Nora and Charlie amidst a sea of panicking Georgians. The city's devolved into chaos, but they're determined to stop that bomb from detonating...
In a flashback, to nine years after the blackout, Miles welcomes Alec back after he returns from a mission. Alec's mission was a failure, and Miles is well aware the Monroe Republic can't afford to engage in war with Texas. Since the Texans in question saw Alec's face, Miles has agreed to send him back to Texas as a means of avoiding war. Alec is distraught by the betrayal and begs for his life, knowing Miles' decision is worse than death for him. Miles coldly sits back as Alec is dragged out of his office, to an uncertain but gruesome fate.
Late that night, Jane catches Rachel searching through her files in hopes of uncovering the key to turning the power back on. Jane implores Rachel to drop her quest - after all, the nanites kept Danny alive just as they did Beth. Rachel did terrible things in an effort to keep Danny alive, and now that he's dead, none of it mattered. If she could do it all over again, she'd sacrifice Danny. Unable to believe this and willing to do anything to save Beth, Jane advances menacingly with her blinking device. But Beth has heard everything. Incredulous that Jane has always known how to turn the power back on, Beth threatens to slit her wrists if Jane doesn't give Rachel the knowledge she needs to destroy the nanites. Jane hands Rachel a thin notebook, telling her, "Get out. And don't come back."
Miles notices Alec climbing a nearby fire escape with the bomb and goes chasing after him with Nora and Charlie. Inside the building, Miles finds a resigned Alec sitting next to the bomb. Alec fully intends to blow himself up along with the whole city of Atlanta. It's his job - and the job comes first, at least that's what Miles taught him. Miles assures Alec he was wrong, but the damage has already been done. As he's berating Miles for effectively destroying his life - and everything Miles taught him to believe - Alec's walkie-talkie goes off. Monroe orders Alec to execute his mission.
Miles tackles Alec and the two engage in a knock-down, drag-out fight. If Alec gets to that bomb, they're all dead. As the two wrestle on the floor, Miles implores Alec not to carry out his mission, but Alec claims Miles' has done this to him. With no choice, Miles unsheathes the knife he once gave Alec and kills the closest thing to a son he's ever known. Back in Philadelphia, Monroe is furious when Alec doesn't respond to his orders. Later on, as Miles quietly broods, Charlie asks Miles about what he did to her mother. She just wants to know the truth. Miles says the truth is people count on him, and they get hurt - and that's because he doesn't even think twice about hurting people... that's just who he is. Disgusted with himself, Miles tells Charlie to get the hell away from him.
President Foster orders Miles to return the bomb to her office, where she asks him for the radioactive material that powered the device. Miles refuses to hand it over, assuming she'll just nuke Monroe right back. President Kelly informs Miles of her money, her tall ships and her plans to attack Monroe's Southern border. She wants Miles to strike at the Republic from the inside. But Miles doesn't have that kind of manpower, even on his best days. Outside, President Foster shows Miles a platoon of 200 men, with over 1,000 weapons. Is Miles ready to be a general again?