On August 10, 2010, a.t.b., Japan was conquered by the Holy Empire of Britannia. Seven years later, teenage student Lelouch Lamperouge finds himself pulled into a battle between anti-government terrorists and the Britannian Army in the Shinjuku Ghetto. In the midst of the conflict, a mysterious, green-haired girl saves him from death by granting him "the power of the king", which allows him to compel others to do his bidding.

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.

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.

Back at Ashford Academy, Sayoko Shinozaki is posing as Lelouch. Realizing the Eunuchs are not interested in saving Tianzi, Li Xingke rebels. As the Black Knights hold their ground against the Chinese Federation and Britannian forces, Zero tries to reason with the Eunuchs, who openly admit their treachery. When Xingke tries to shield Tianzi from the fighting, Zero personally enters into the field with his new Shinkirō Knightmare Frame. Diethard hacks into the Chinese media network and replays the Eunuchs' deceit, igniting riots across China. Faced with open rebellion, Schneizel orders a Britannian retreat and Xingke eliminates the Eunuchs and rescues his comrades. However, Kallen and the Guren have been handed over to Britannia. With the Eunuchs dead, Zero forges an alliance with Xingke and Tianzi. Lelouch returns to Ashford Academy, and is surprised to find Anya and Gino enrolled as students.