Miles's life is in grave danger as he finds himself in the clutches of Titus Andover. Charlie is determined to find Monroe, as Rachel and her father, Dr. Porter desperately attempt to revive Aaron. Meanwhile, Neville hatches a plan to infiltrate the Patriots.

Monroe and Charlie's dynamic begin to evolve. Meanwhile, wounds of Miles and Rachel begin to heal, yet her curiosity and heightened awareness could be her undoing. Neville's manipulation of Patriot power brokers makes Machiavelli look like a cherub and Aaron's mind works overtime awake or asleep with mind-blowing effectiveness. Rachel and Miles begin planning a resistance to what they believe might be the Patriot occupation.

As Charlie, Rachel and Gene question Monroe's true allegiance, Miles himself is weary of his former friend's intentions. Meanwhile, Aaron continues to have visions that lead to endless questions.

As Miles and the gang try to escape the perils of their current situation, Rachel and Gene continue to struggle with their relationship, which affects Charlie. Meanwhile, Neville takes a gamble with the Patriots.

When Miles leads Monroe and Rachel south of the border; they're met with much more than they bargained for as Neville and Julia dance a delicate dance. Meanwhile, Charlie and Gene continue their search for Aaron.

When Gene decides to assist the town of Willoughby, Rachel and Charlie feel compelled to help too as Miles and Monroe continue to join forces in order to survive.

With their lives in danger in New Vegas, Monroe and Connor face a difficult decision in order to survive. Back in Willoughby, Miles questions whether he can trust Neville and Jason to help take down the Patriots. Meanwhile, Aaron and Priscilla find themselves at odds over the nano code.

Monroe, Charlie and Connor make their way back to Willoughby, where they find that the Patriots' reeducation center is up and running. An encounter with two of the center's young cadets leaves Rachel and Miles divided on the lengths they are willing to go in order to take down the Patriots. As Neville and Jason find a new ally for their mission, more about the history of the Patriots is revealed.

Frustrated with Neville, Jason turns to Miles with crucial information about the Patriots’ next steps for Texas. Determined to derail the Patriots’ plans, Miles and Monroe rush to Austin with Jason, Charlie and Connor in tow. Meanwhile, Aaron grows suspicious of Priscilla’s increasingly unusual behavior.

Truman, empowered with new authority from the President, launches a mustard gas attack designed to kill Miles and Monroe. To Rachel's disappointment, Miles agrees to join Monroe in a ruthless plot to beat the Patriots at their own game. As Neville faces his own challenge from the Patriots, Aaron grows increasingly alarmed by the power of the nanotech.

Miles, Charlie and Monroe launch an attack on the Patriots, but must improvise a risky new plan in order to halt the oncoming war between California and Texas. Out for revenge, Neville sets his sights on President Davis. Meanwhile, Aaron and Rachel’s efforts to save Priscilla from the nano-tech has unexpected consequences.