The Patriot Act
Rachel secretly digs up Monroe's casket and opens it up... He's alive! In a safe house, Rachel informs everyone that she injected Monroe with a barbiturate that merely knocked him out. He'll be himself in a few days. Suddenly, an explosion rips through Willoughby and blows a store to bits. Three people are killed and dozens are wounded in the chaos. After tending to the injured, Dr. Porter confronts Truman about his suspicion that it was a terrorist attack by the Patriots, but Truman warns the doctor to stay in line before giving a speech to the townspeople that blames the attack on the Andovers. In the meantime, Willoughby will be sealed off and placed under curfew from dusk 'til dawn.
Dr. Calvin Horn, a former DOD co-worker, approaches Rachel. Having fled the capitol with Flynn after the Blackout, Horn has become the president's senior science advisor. He's the one who put Rachel on a wanted poster because he needs to know more about the nanites. Have they been modified to release energy, thus burning two men to death? And why are the nanites acting strangely only in Willoughby? Rachel plays coy, but Horn knows better. If Rachel doesn't know... then who?
Rachel warns Aaron that since the Patriots found the bodies he incinerated with his thoughts, it's only a matter of time until they find him too. Miles says they need to get Aaron out of Willoughby with Monroe's help before something happens, but Aaron refuses to leave unless Cynthia comes too. This seems impossible since the Patriots have the town on lockdown, but Aaron demands Miles figure out a way to make it happen.
In a flashback, Dr. Porter stands with other townspeople on the edge of a mass grave, seven years after the Blackout. As the local doctor, he oversees the cremation of dozens of wrapped corpses, all dead of cholera, his wife among them. At home, Martin Shaw waits, promising a truckload of cholera vaccinations if Porter will help restore the "country he loves." Back in the present, Porter meets with Horn, who seems to be oddly obsessed with Rachel. Spying a pin on Horn's lapel - a stylized Eye of Providence - that brings terrible flashes of memory, Porter claims it's all business as usual with Rachel.
Across the country, Neville and Allenford have Jason tied up in the warehouse. When shots ring out, Neville realizes the Patriot cadets are closing in. Jason asks to be set free, but Allenford insists that if they release him, the young man will kill them both. After a pause, Neville puts a knife to Jason's throat, promising to use it if Jason blinks wrong. Neville unties Jason and prepares for war. Upon exiting the warehouse, Jason raises his hands and calls out to the cadets; he claims he's been abducted, then ruthlessly kills them all. Allenford and Neville nervously approach Jason, expecting the worst, but he simply hands his bloody knife to his father: a sign of trust.
In a flashback, Porter recalls the first time he saw the Eye of Providence, working with Shaw and the Patriots. Although he joined them for the right reasons, Porter finds himself assisting in torture and killing. Right and wrong have become all wrong, even if he's keeping the people of Willoughby alive. In the present, guilt compels him to aid in Aaron's escape. As Aaron and Cynthia pack up and prepare to leave, together, Shaw shows up at Porter's door to drag him to an audience with Horn.
Horn drills Porter: how did Aaron Pittman come back to life? Porter claims he doesn't know, but Horn demands he start speaking up or townspeople will die. Stuck between a rock and a hard place, Dr. Porter tells them his Rachel isn't controlling the nanites, Aaron is. And he promises to bring them to Aaron's hiding place. Outside Willoughby's walls, Porter points to a couple - not Aaron and Cynthia - as Miles and Rachel watch through binoculars. Rachel feels sick to her stomach; her dad is... one of them?
Neville, Jason and Allenford set up camp a few miles from where they were ambushed. Allenford wonders if she can get to her son in Cincinnati, but Neville doesn't know if that's a good idea. Suddenly, Allenford passes out. Jason looks at his father... what did he give her? Later, Neville pours water on Allenford to bring her around. She was worried about Jason this whole time, when she should've been worried about him. Now Neville demands to know - where is Allenford's husband?
Miles and Rachel spring into action. They reach Aaron and Cynthia before the Patriots do, but Truman and his men are out in full force searching for them. Porter reluctantly moves along with the Patriots as they hunt Aaron down. Miles locates a sewer and works with Aaron to get the whole group into it just as the Patriots burst in looking for them. The group crawls through the sewage pipe in hopes of finding an exit. But when they do, Aaron opens up a portal to the outside only to find two Patriots pointing guns at him.
Aaron and Cynthia are surrendering when Monroe bolts out of nowhere to cut down the Patriots. He didn't plan for reinforcements, though, so when more troops swarm in, he takes off. When the Patriots seize Aaron and Cynthia, Aaron begs for mercy, but no one listens. Fuming, Aaron focuses on the guard holding Cynthia, and the man quickly bursts into flames, horrifying Cynthia. Finally, she fully understands what he's been talking about - and Aaron understands that she's deathly afraid of him. Back in Willoughby, Rachel is devastated, unable to cope with the realization her father is working with Horn and the Patriots. Across town, an unhappy Truman warns Porter that if they don't find Aaron soon, he may not be able to control himself when it comes to Rachel.