After managing to capture Cornelia, Lelouch forces her to reveal what little information she knows of Marianne's murder, but the answers do not please him one bit. V.V. takes Nunnally to Kaminejima, and Lelouch abandons the Black Knights to rescue his sister. Without Lelouch, the Black Knights begin to lose ground to the Britannian Army. Suzaku follows Lelouch, leading to a final confrontation between the former friends.

One year after the Black Rebellion, Lelouch Lamperouge has resumed his normal school life with no apparent memories of the year before. After skipping remedial gym class, he sets off with younger brother Rolo to gamble at Babel Tower. Led by C.C., the Order of the Black Knights launches an attack on the complex to retrieve Lelouch. C.C. reawakens Lelouch's memories, and he resumes his identity as Zero. Suzaku Kururugi declares to the Emperor that he will personally kill Zero.

Lelouch directs the Black Knights in a counterattack against the Britannian forces and recalls how he came to forget his past: after Suzaku arrested him and brought him back to Britannia a year ago, the Emperor used his Geass to implant false memories in Lelouch's mind. The new Knightmare Frame prototype Vincent arrives and wreaks havoc on the Black Knights. They collapse Babel Tower to retreat, simultaneously dropping it on Viceroy Carares and creating a road straight to the Chinese Federation Consulate, where the Black Knights escape to. Zero broadcasts his plan to recreate the United State of Japan. The Britannian military retreats, but the pilot of the Vincent, Rolo, is not so easily swayed. After arriving at the consul grounds, he confronts Li Xingke, revealing that he too possesses the power of Geass.

Suzaku returns to Ashford Academy to investigate Lelouch. With the Black Knights reassembled, Lelouch plans to lead the resistance while maintaining his façade as a student. A welcoming party is held for Suzaku at the academy, and C.C.'s love of pizza threatens to reveal Lelouch's secret; Kallen arrives to retrieve her but is seen by Villeta. She tells Lelouch how she came with Kaname Ohgi the previous year, and Lelouch uses this information to blackmail her. Alone, Suzaku reveals to Lelouch his goal of becoming the Knight of One, which would allow him complete governing authority over Area 11. To test Lelouch, he allows him to speak with the new Viceroy of Area 11: Nunnally vi Britannia.

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.