In the aftermath of a new catastrophe Rachel deals with the part she has played, while Miles confronts a new form of lawlessness. Charlie embarks on her own mission in the Plains Nation when she finds a lead on Monroe's whereabouts, and Tom and Jason go in search of a lost loved one.
Miles finds himself a prisoner of the ruthless leader of a separatist group, while Neville acquires intel about the Patriots. Meanwhile, Charlie attempts to infiltrate those who have captured Monroe, and Aaron's shocking recovery leads to more questions about life and death.
Willoughby is besieged by Titus Andover's people after a prisoner escapes with something precious, forcing Miles to negotiate with him. Neville and Jason find it difficult to infiltrate the Patriots, and Monroe confronts Charlie with news about her mother.
Rachel becomes suspicious of the Patriots, who are now occupying Willoughby as the town's saviors. Monroe surprises Charlie by coming to her rescue, and Neville finds a way to advance within the enemy's ranks.
Charlie and Monroe arrive at Willoughby, where they find Miles looking for a way to start a war between Texas and the Patriots. Aaron considers the new implications of his nanotech experience, and Neville gets closer to Secretary Allenford.
In the midst of his attempts to start a war Sebastian Monroe is captured by the Patriots. Elsewhere, Tom comes face-to-face with his son -- brainwashed into a killer by the enemy's black-ops re-education center.
When Aaron becomes the target of a dangerous Patriot scientist his friends attempt to smuggle him out of town, and Rachel's father attempts to use his position to atone for his past sins.
Miles and Rachel plot a chemical attack on the Patriot leadership, only to find that her father will be among them. Neville tries to manipulate Secretary Allenford's husband, and Aaron falls into the dangerous hands of Dr. Calvin Horn.
The group continues to search for Aaron after finding the entire Patriot detachment in Willoughby unconscious, while Aaron himself discovers a way to communicate with the nanites. Elsewhere, Neville learns the truth about his wife's fate.
Miles reluctantly agrees to help Monroe locate his son, who was secretly sent away into Mexico as a child. Tom and Julia undertake a plan to elevate his position among the Patriot hierarchy, and Aaron sets out with a clue left by the nanites.
Monroe's newly rediscovered son makes it clear that he wants nothing to do with him when he takes him to his boss, and Rachel and Miles must mount a reluctant rescue. Meanwhile Neville finds a new reason to take down his wife's new husband, and Gene tries to rescue a friend from the Patriots.
Gene, Charlie, and Rachel are drawn into a disease outbreak at Willoughby, which Rachel discovers is not what it appears. Elsewhere, Tom and Julia put their tenuous positions at risk in hopes of rescuing their son.
Monroe leads Charlie and Connor on a dangerous mission to his old scene, and Neville gets a new assignment from the President. Elsewhere Aaron and Priscilla reunite with an old friend, who has found his own remarkable use for the nanites.
Held captive in New Vegas, Monroe and Connor learn that they will be forced to fight to the death. While Miles debates how far to trust his new allies, Aaron and Priscilla debate whether or not to help save the nanites from an inevitable destruction.
Aaron awakens to find himself in a world with power, where he is still married to Priscilla and running his company -- only to learn that the nanites have created a virtual world to get what they want from him.
Miles and Monroe capture a pair of young recruits from the Patriots' reeducation center, leading to a conflict over how far they are willing to go to defeat the enemy. Aaron and Priscilla make their way home, and Neville must come up with a new plan to capture Monroe after Miles refuses to help him.
Gene and Miles venture into Willoughby in the hopes of finding allies to stand with them against the Patriots, only to find themselves trapped right under Trueman's nose. Meanwhile Monroe and the others find more men, and Neville attempts to turn Trueman against his superior.
A frustrated Jason turns his back on his father and joins Miles and Monroe, traveling with them to the Texas capital on a mission to stop the assassination of the president of the Republic. Meanwhile, Priscilla explores her connection with the nanites as she and Aaron travel to Willoughby.
Miles has a very bad day, beginning with a bloody confrontation with the Texas Rangers that leads to him being wounded, trapped, and alone. While Charlie, Rachel, and Monroe search for him Charlie is confronted by Neville, who demands to know the whereabouts of his son.
After the Patriots attack the rebel's encampment with mustard gas, Bas and Miles attempt to steal a chemical weapon to hit back at the enemy. Aaron grows more disturbed by the nano-tech, and Neville is on his own when the Patriots send a man to kill him.
Miles' and Monroe's two groups find themselves at cross purposes after stealing a shipment of mustard gas from the Patriots. Rachel learns the truth about Priscilla and comes face-to-face with the nano-tech.
With one crisis averted Miles comes up with a risky plan to kidnap President Davis in the hopes of stopping a war between Texas and California -- but he must rely on the loyalty of Monroe. Aaron and Rachel's efforts to free Priscilla from the nano-tech has unforeseen consequences.
