It's been one year since the failure of the Black Rebellion and the supposed death of Zero. Britannia has assigned Area 11 a "correctional education" status, where Elevens are made an example of by brute force, to try to prevent any future uprisings and suppress rebellious thoughts. Unsuspecting high school student Lelouch, oblivious to his rebellious past as Zero, stumbles upon a scheme on his life and the life of a mysterious woman known as C.C., who reveals to him his forgotten purpose and his "true" self. Destroying his assailants and declaring himself Zero once again, Lelouch sets out to finish what he started.

   The Empire of Britannia has invaded Japan using giant robot weapons called Knightmare Frames. Japan is now referred to as Area 11, and its people the 11's. A Britannian who was living in Japan at the time, Lelouch, vowed to his Japanese friend Suzaku that he'd destroy Britannia. Years later, Lelouch is in high school, but regularly skips out of school to go play chess and gamble on himself. One day, he stumbles on terrorists 11's who've stolen a military secret and is caught by a member of the Britannian task force sent after them, who is Suzaku. As the rest of the squad arrives, Suzaku is shot for disobeying orders, while the military secret, a young girl, gives Lelouch the power of Geass, which makes anyone obey any order. While Suzaku is secretly made the pilot of Britannia's brand new prototype Knightmare, Lancelot, Lelouch becomes the masked Zero to lead the rebellion to destroy Britannia once and for all.

   In a future where the world has been ravaged by a nuclear apocalyse, there exists salvation in a domed city named "Romdo", where humans and their android servants, the AutoReiv, live in. Under the implementation of complete management control, it is a paradise where feelings are literally discarded, and the governing council dictates the way of life the citizens should live. But this utopian landscape is soon broken by a series of mystifying murders. Re-l Mayer, a female inspector from the Citizen Information Bureau, along with her autoreiv partner Iggy, are tasked to solve the murder cases. She is soon attacked by a creature drawn to her which is neither human nor android, and learns about the mysterious phenomena called "Awakening", an event which draws her further into the case...and to the world beyond the limits of Romdo.