Lelouch begins his reformation of Britannia, abolishing the aristocracy and Area system. The Knights of Rounds attempt to remove Lelouch from power, but Suzaku, piloting the Lancelot Albion, easily obliterates their ranks, killing Bismarck Waldstein and two other Rounds members while only disabling Gino's Knightmare. His position secure, Lelouch announces his intention to join the U.F.N. On the way to the meeting, he and Kallen bid each other farewell after she kisses him, Kallen having been unable to get Lelouch to answer any of her questions. When the UFN demands that he accept a limit to his voting power to prevent Britannia from attaining an automatic majority, Lelouch forces their hand by having Suzaku take the U.F.N. leaders hostage and Britannia's military surround Japan. During the commotion, the Britannian capital is obliterated by Schenizel, who is aboard his new flying fortress, the Damocles. He reveals to Lelouch that Nunnally is alive, and she declares herself to be Lelouch and Suzaku's enemy.
Schneizel unveils his plan to position the Damocles in such a way as to strike every warring nation in the world, thus enforcing peace through the threat of annihilation. Cornelia objects, but is gunned down. Lelouch declares Nunnally his enemy during their conversation, but in private has trouble with the thought of fighting her. With some harsh words from Suzaku and C.C.'s comfort, Lelouch comes to his senses and focuses on his original task. Nunnally, frustrated that she cannot fight or protect anyone, decides to shoulder the sin of launching F.L.E.I.J.A. herself. Schneizel, backed by the Black Knights and the remaining Knights of Rounds, clashes with Lelouch in the sky above Mount Fuji. Though Lelouch is able to destroy a fair portion of the Black Knights by detonating the sakuradite mines in Mount Fuji, the Damocles remains unassailable and its payload of F.L.E.I.J.A. warheads still looms over him.
The Black Knights manage to board the Avalon. Lelouch escapes in the Shinkirō while C.C. holds Kallen at bay long enough for Lelouch to escape. Using Nina's F.L.E.I.J.A. Eliminator, Lelouch and Suzaku successfully break into the Damocles. Believing Lelouch to be trapped, Schneizel sets the Damocles' self-destruct sequence and attempts to leave. However, Lelouch manages to outsmart Schneizel, using his Geass to force him into obedience. Suzaku and Gino battle outside the fortress, with Gino unable to hold out against Suzaku. Using his last attack, Gino takes out the Damocles shields, allowing Kallen to take over. Meanwhile, Lelouch goes to confront Nunnally, who has regained her sight.
Lelouch and Suzaku fight for the sake of their promise, the Zero Requiem. Suzaku battles Kallen, while Lelouch confronts Nunnally, his biggest and dearest enemy.