After fleeing the Union, Alice is a fugitive again. Father John and the Sergeant are after her, hoping to capture her, reboot her brain, and extinguish the threat she represents to the authoritarian system they both want to establish. On the run, Alice and her friends take refuge in the Android Zone, a safe territory created by her friend Max and the survivors from Central City.
One morning, Father John reaches them and threatens Alice, telling her he’ll attack the city if she doesn’t surrender. But she’s fortunate enough to find a memory machine, and warns her father she’ll use it if necessary. Scared she will erase his memories, he decides to abandon his plan. But days later, Alice gets ill, and Max, worried, calls the only person who can save her: her father John, who cures her, but kidnaps Jake as a hostage. With the help of her friends, Alice frees him, but Rhett dies in the attack. Saddened by the loss of her boyfriend, she hatches a plan for revenge, triggering a fight between the soldiers from the capital and the citizens of the Android Zone. During the fighting, Alice realizes Rhett is still alive, and is now an android like her. Max’s side wins the battle, and he and Alice rebuild the territory so that humans and androids can live as equals.