After the initial shock of seeing Aaron wears off, Grace explains she's been living alone in Spring City since The Tower. And there's another surprise in store for Aaron: his wife Priscilla is passed out on Grace's couch. It turns out she's been suffering from visions similar to Aaron's - the fireflies, dead people, etc. - and her dead father told her to find Grace. In fact, Grace's husband thought she was so crazy that he took the kids and abandoned her.
Grace knows the nanites directed the couple to her. Clearly the nanites have crossed into consciousness; perhaps they have even learned to network. Since Aaron wrote the original code for the nanites, he gave them their "mind," and since Priscilla helped, well, she's like their mother. Priscilla wonders why their friend Peter, who also helped write the code, wasn't called to Spring City too. Regardless, the nanites are everywhere, and apparently they have a mind of their own. What Grace wants to know is how does all this make the nanites any different from God?
Connor takes Monroe to Nunez's opulent villa, where a flayed corpse is displayed as evidence of what happens to those who do the boss wrong. It's clear Nunez relies on Connor, whom he's raised like a son, and he's pleased with the offering of Monroe. When Nunez asks Connor for his take on Monroe's fate, Connor suggests selling him to the highest bidder. Lucky for Monroe, Miles and Rachel are already plotting his rescue. However, when Miles reaches him, Monroe refuses to leave, preferring to stay so Connor can take credit for his capture. Unfortunately, Miles is captured, too, and dumped alongside Monroe in a locked cell.
Charlie and her grandfather spy on Truman and the Patriots as they erect a large armed camp. Porter spies his old friend, Welliver, and wants to retrieve him immediately, but Charlie knows there's no way. Who'd have thought Porter had the same stubborn spirit as Rachel? Late that night, Porter sneaks into the Patriot camp, only to discover Welliver is already dead. Having guessed Porter would go after his friend, Charlie rescues him from a guard. Moments later, they're both captured.
Neville delivers congratulatory flowers to Julia, an excuse to ask whether she's yet forced her husband to hire Neville onto his security detail. She hasn't. Neville is further annoyed to discover Jason has stolen documents from Allenford that lay out plans for numerous reeducation programs - all run by Julia's husband Doyle. Having survived the torture of reeducation himself, Jason is adamant - something must be done! Late that night, Neville tells Julia that Doyle is responsible for nearly killing Jason. Now he wants her to get him into Doyle's office to steal what he needs to blackmail his way onto the security detail. Julia warns that she may not be able to protect Neville if he sneaks into Doyle's office, which feeds Neville's paranoia: whose side is Julia on?
Miles and Monroe argue long into the night. Monroe wanted to give Connor something, some help, and all he has to give is himself - which has of course screwed Miles. Inside his inner sanctum, Nunez toasts Connor to celebrate the capture of Miles - a matched set means more money. Somehow, Nunez can't believe Connor rescued Monroe, the most ruthless man in the world. As a test, he has Connor whip Monroe, who's strung up in front of a crowd. Just when things are closing in on fatality, Connor halts the proceedings, asking, "Do we want to sell him? Or bury him?" Nunez's greed wins out.
Rachel has just bribed her way into the inner sanctum when Connor hands her the key to Miles and Monroe's cell, unaware that another of Nunez' henchmen is watching. The three are just running off when they're stopped by Nunez, who has a knife to Connor's throat. Nunez can't have anyone thinking he's weak and Connor made his choice. When Connor makes a move, Miles, Monroe and Rachel back him up. After they escape, Connor claims helping Monroe was the first mistake of his life. But... does Monroe really think he can regain all the power he lost? Monroe promises that together, father and son will take back the power - and more.
Back at the White House, Doyle calls his security detail into his office - someone broke in! Now he'll need more security! Fearing Neville has gone ahead with his plan, Julia sneaks into the soldiers' camp to scold him, only to realize it was Jason who broke into Doyle's office. Furious that his parents continue to scheme will the country is going to hell in a Patriot handbasket, Jason admits his crime, just as soldiers come to detain him for questioning.
Truman uncuffs Charlie and Porter, hands them masks and ushers them into tent sheathed in plastic. It doesn't take Porter long to realize Truman has a typhus epidemic on his hands - and this is just the beginning. Porter's friend Welliver was the first, and now Truman and the Patriots are rushing to build a quarantine camp in advance of the inevitable outbreak. Porter and Truman may have their differences, but now it's time to work together, or else the town of Willoughby will be lost.