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.
The story is located in a colony "Industrial 7" in UC (Universal Century) 0096. It depicts an encounter of a 16 years old student Banagher Links and the pure white mobile suit "Unicorn Gundam", and also depicts the global basis war over the forbidden box "Laplace".
After discovering that Neuroi are capable of communication with humans and making peace with the nest above Gallia, the Witches squads are now on a mission to re-establish communication when the Neuroi completely vanish after a sudden attack. It is then that they discover a new massive nest that just appeared covering almost all of Europe. Ruthless and without mercy it annihilates allied forces along with many Witches. Word of the attack reaches Fuso and a support battalion is deployed to rescue the survivors. Among the rescue team is the former Striker captain Sakamoto Mio and the now civilian Miyafuji Yoshika who wants to save her dear friends.