As Aaron and Priscilla rekindle their relationship on the road home, the action picks up in the middle of the Matheson/Neville standoff. Neville wants to know whether Miles is willing to lay his life on the line for Monroe. That's when a twig snaps, giving Miles and Rachel the opportunity to run off. Neville and Jason are left to confront Doyle and a squad of Truman's Patriots, who pursue Miles, only to wind up dead. The next day, a contemptuous Neville demands more men and a free hand, but Doyle refuses. Booting Truman out of his own office, Doyle lays into Neville: even though the president spared him and Julia, Doyle will have their heads as soon as he finds Monroe.
A week later, Miles and Rachel catch up with Monroe, Connor, Charlie and Duncan's soldiers and retreat to an abandoned hydro plant. Miles fills Monroe in on Neville's quest to save his wife, then takes him to check out a new development: while stockpiling weapons, the Patriots have recruited all of Willoughby's youth for cadet training. Hearing a twig snap, the two men quickly flush two terrified escapees from the brush, Kim Carson and Dillon Matthews. Back at the safe house, Porter quickly recognizes the kids and knows something's wrong with them. Miles and Monroe discuss hitting the munitions dump, which will likely involve collateral damage - the town's children. Rather than allow Monroe to interrogate their captives, Rachel and Porter eventually coax out some information. Kim claims all Willoughby's kids enlisted under their own volition. When Rachel and Porter arm themselves and prepare to take the kids home, Monroe gets feisty. Claiming he'll handle it, Miles puts Monroe off and heads out after the group. Little does everyone know, Neville and Jason are spying on the camp and scheming how to use trouble in paradise to their advantage.
In the Oval Office, Roger Allenford tells President Davis that Willoughby's Reeducation Center is up and running. Mincing no words, the president orders Allenford to take out Monroe and the Mathesons so the cadets' mission can begin. It's time to overthrow the Commander of Texas, General Carver. And if Allenford isn't with the program, the president is perfectly happy to shoot him, Doyle and both their families. Meanwhile, Neville pays Truman a visit. Doyle is sending men after Monroe, but only Neville knows where he is. If Truman will give Neville the men needed to capture Monroe, Neville will back his play to control Willoughby. Truman flashes back to his time as a Guantanamo prison guard in the days after the Blackout. Just when things seem like they can't get any worse, the remnants of the U.S. government appear in the harbor in the form of a ragtag flotilla.
Kim's dad, Grant, aims his rifle at Rachel et al. when they show up at his door. Porter tries to explain something is very wrong with the training camp, but Grant believes Miles and his crew are terrorists, per the Patriots' propaganda. That's when Kim spills her guts: the Patriots blindfold the kids every night and when they wake up in the morning... none of them can remember what happened. In fact, Kim's black eye came from her time in camp. Grant takes a closer look, only to find a number tattooed inside her eyelid. When he repeats the number, Kim grabs a shotgun and shoots him in the back without blinking, then slits her own throat.
Back at the hydro plant, Rachel examines Dillon, who also has a number tattooed in his eye socket, which sets everyone to arguing over what to do with him. It's just the opportunity Neville needs to attack, during which Charlie comes face-to-face with Jason for the first time in months. Without hesitating, she knocks him out. During the chaos, Rachel unties Dillon and tells him to run, begging Miles not to shoot him. After beating on Neville, Monroe runs after Connor, who's being trounced by Jason. In the end, it's Miles who covers everyone's escape. The next morning, Doyle rips into Neville and Truman for their failure. It takes Truman back to Guantanamo when he stood next to Allenford while Jack Davis proposed a coup to kill the Vice President, the only senior U.S. official left alive after the Blackout. They'll build a new America with new ideals - a new order for the ages! Davis introduces DOD consultant Victor Doyle, who makes a scary promise to win hearts and minds.
At a new safe house, Monroe scolds Miles for sparing Dillon. Monroe admits to wanting revenge for the destruction of Philadelphia, but Miles isn't clear on Monroe's bottom line. Isn't all this because Monroe wants his Republic back - a sort of new family business? Monroe doesn't deny it. He knows what he's fighting for, but does Miles? Back in Willoughby, Doyle orders Jason into his office. Pulling down his eyelid, Doyle invokes the power of the number tattooed there, then asks a zombified Jason to tell him everything about his father.
While the Nevilles scheme to capture Monroe, Rachel and Miles uncover the Patriots' nefarious new plan to re-educate Willoughby's youth.