Plot

Miles and Company are trapped in Willoughby. When Rachel discovers some unsettling truths, Miles does what he does best to overcome obstacles before him and those he cares about. Meanwhile, Charlie shares a moment with her mom, as Neville and Jason continue their struggles between father and son.—Anonymous

Someone new has arrived in Willoughby, Dr. Calvin Horn and he wants Rachel to explain how she is controlling the nanos. The mole however informs Horn that it's Aaron Pittman who is exercising control, not Rachel. They set a trap to take Aaron hostage but Rachel are Miles are one step ahead of them and learn the identity of the mole: Rachel's father Gene Porter. Aaron and Cynthia manage to get away with help from an unexpected source. In flashbacks, Gene's motivation for working with the Patriots is revealed. Tom Neville has taken his son Jason prisoner but Justine Allenford says he's dangerous and can't be let loose. When they are attacked by other Patriot cadets, Jason shows his true colors.—garykmcd

We open with Rachel digging up Monroe and telling him "don't move." He's brought to a house just outside of Willoughby where we learn that Rachel gave him enough barbiturates to make it seem like he was dead. Monroe is groggy, sounding almost drunk, but he should be okay in a few days.

Aaron and Cynthia walk down the street arguing over the restrictions the Patriots are placing on their teaching. Suddenly a bomb blows up the building just behind them. They are okay but dozens of people are badly injured.

Gene goes to see Truman. He's convinced the Patriots are behind the bombing and wants to know why. Truman doesn't appreciate Gene's tone and reminds him his job is to be loyal.

Truman addresses Willoughby, telling everybody that another outside element has infiltrated the town but they are doing their best to find who is responsible.

A Dr. Calvin Horn arrives in town, wanting to speak with Rachel. He worked with her back at the Defense Department and is now the President's chief science advisor. He's responsible for the Wanted poster with Rachel's name, saying he wanted to seek her out for info on the nanotech. He's there because of the two men who burst into flames and thinks it's possible the nanotech could be engineered to release the energy it stores. Rachel says she's not responsible but Horn doesn't seem convinced.

Rachel and Miles warn Aaron about Horn snooping around. They suggest he disappear and let Monroe take care of him. He demands they find a way for Cynthia to come with him. We see that Gene is listening to this entire conversation through a grate in the next room.

SEVEN YEARS AFTER BLACKOUT -- Gene and dozens others stand over a mass grave and lights the bodies on fire. Gene walks back to his home and finds a man waiting for him. He has a high quality vaccine for cholera, the very disease that killed all of those people including Gene's wife. He says he has hundreds of vials and his interest in Gene helping him take his country back.

Jason wakes up and Tom gives him something to help wash out the drugs. Jason seems better, but Allenford thinks it's an act. She says "you can't fix him." They hear gunfire in the distance and Jason asks Tom to remove his leg restraints so he can help. Over Allenford's objections he does it.

Monroe gets dressed and sees Miles signaling him from town with a mirror.

Gene meets Horn with Truman at Patriot HQ. The insignia on Horn's jacket flashes Gene back to terrible memories that include torture. Gene ends up lying to Truman and Horn and says Rachel hasn't said anything yet.

While watching people in town Gene flashes back to nine years after the blackout. He watches as a man being water boarded begs to go home. Gene is asked by the man who approached him with the vaccines, Shaw, to keep this man awake chemically so he can be tortured further. Later he tells Shaw what they're doing goes "too far." Shaw reminds him they are the "good guys."

Rachel, Miles and Charlie discuss some strange movement of Patriot troops. They don't know how to get Aaron out of town, but Gene walks in and says he'll help. Gene's plan is to sneak Aaron out during his regular trip for meds. Rachel hates it but Gene says he has to do something to help.

Tom, Jason and Allenford are fired upon by some of the cadets. Tom ends up being pinned down in the open and runs out of ammo. Jason stands up and shows his cuffs, saying he's a Patriot and a captive. He walks towards the cadets and calls for Tom to come out. Jason has killed the two cadets who were firing on them.

Aaron and Cynthia prepare to leave.

Shaw walks into Gene's office and tells him Horn wants to see him. Horn wants to know about Aaron. Horn wants to know how he was able to come back to life after Gene pronounced him dead. Horn thinks the explanation must be nanotech and wants to know how Rachel did it. Horn can't find Aaron and wants information from Gene. Gene is having doubts about his work with the Patriots but Horn reminds him of his past. Horn says if Gene doesn't give him information he'll start killing townspeople while he watches. Gene tells Horn and Shaw that Aaron is the one controlling the machines, not Rachel. Horn asks again for Aaron's location.

Horn and several Patriots wait around the corner while Gene waits for Aaron and Cynthia. The couple is a no-show.

We see that Miles and Rachel are watching this from afar with binoculars. Miles had suspected that Gene was working with the Patriots. Miles figured out that Gene must have been supplying them with info for some time.

Allenford tells Tom she wants to head north and seek out her son. She's amazed by what happened with Jason and want to give it a chance with her child. She passes out.

Horn rightly guesses that Gene's cover has been blown and asks "I wonder what your daughter will think of you now?"

Miles and Rachel see if they can move Aaron through the sewer. Simultaneously Horn looks at the city plans and wonders about the sewer. Aaron and Cynthia get down the manhole just before Truman and Horn arrive.

Aaron and Cynthia arrive at a ladder. They climb it and open another manhole, finding themselves staring at two men with assault rifles. Monroe arrives to kill both of the soldiers. But even more arrive and Monroe runs off. As they attempt to place Aaron and Cynthia in custody they explode into flames. Monroe comes back in time to survey the scene. Aaron and Cynthia stare at one another.

Tom wakes up Allenford, who is in cuffs. He wants to know where her husband is located.

Cynthia seems now to be fearful of Aaron.

Gene promises Horn he'll find Aaron. Horn makes a threat that he may hurt Rachel if he doesn't.

Rachel begins crying and Charlie comforts her. They embrace.