The Warden is dead. Coming to terms with the blood on his hands, Conthan finds himself alone. But before he succumbs to crippling self-doubt, he declares war on the synthetic army. Attempting to seize power from the president, a secret society instigates a civil war on American soil. Innocent blood is shed. After a sanctuary for people with abilities is targeted and decimated, the Nighthawks are left seeking vengeance. But when the diary of a psychic is discovered Conthan realizes their actions could destroy the country they are fighting to save.
It's been one year since the incident shut down the Facility. The Nighthawks have started searching for lost Children, rescuing and relocating to an abandoned town. A century old society reveals themselves and stages a coup against the President while the Nighthawks find themselves caught in the crossfire.