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.

Cornelia sets a trap for Zero at the Saitama Ghetto as she begins to clear another resistance cell. Despite C.C. trying to stop him, Lelouch takes the bait and goes to the aid of the Saitama resistance. His plan falls apart from a combination of Cornelia's superior tactics and the resistance cell's dissimilar motivations. Lelouch is cornered and nearly discovered, but C.C. dons his Zero costume and distracts the Britannian Army, allowing Lelouch to escape. Lelouch blames his defeat on the undisciplined rebels and resolves to build something better than a mere resistance unit.

Kallen and Lelouch separately reflect upon the deaths of innocents in the Narita campaign. Shirley secretly follows Lelouch and witnesses the battle between the Japan Liberation Front and the Britannian Army, which Lelouch ends by detonating the Japan Liberation Front freighter as the Britannian Knightmares begin to board it, killing all personnel on board and giving the Black Knights the element of surprise. Suzaku attacks Lelouch, easily overpowering his weaker Burai with the Lancelot, forcing him to eject. He crash-lands near Shirley and is knocked unconscious. Shirley prepares to kill him to avenge her father, but hesitates when his mask falls off, revealing to her that Zero is Lelouch.

The Ashford Academy holds their annual school festival. Ohgi, Villeta, Euphemia, and Kallen all make their separate ways to the event. A series of close encounters risks the revealing of hidden identities, but all those involved escape. Suzaku pilots the Ganymede for the festival's main event: making a giant pizza, slated to be the world's largest. When Euphemia's presence is revealed, mass panic ensues. On live television, she declares the Mount Fuji area to be the "Specially Administrated Zone of Japan", where Elevens can be referred to as "Japanese" again. She believes this will bring back the happy days with Lelouch and Nunnally, but Lelouch thinks otherwise, knowing she is being naive.

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.

Lelouch is shocked that Sayoko has made him into a playboy. As he tries to work out a way to undo the damage, Milly declares Cupid Day, where any girl can become a boy's girlfriend by stealing his hat. Rolo and Sayoko help Lelouch avoid the female students trying to catch him. Alone, Lelouch and Shirley discuss recent events and trade hats. Elsewhere, Knight of One Bismark Waldstein informs the Emperor of a meeting between the princes and princesses about waging war against the Chinese Federation, where Schneizel decides threats and negotiation will work better than open war. Cornelia, determined to reveal the existence of Geass in order to clear Euphemia's name, confronts General Bartley, who begs her to help them, saying the Emperor's recent actions may destroy the world. While Suzaku and Lloyd discuss on the Guren, Nunnally visits Kallen in prison. Jeremiah arrives in Area 11 and uses his newly-acquired Geass Canceller on Shirley, restoring her memories of Zero's identity.

A ceasefire is called so Schneizel can meet with the leaders of the Black Knights, but Lelouch is too devastated to attend. Schenizel reveals the truth about Lelouch and his Geass, as well as the many people he has used it on; a recording from Lelouch's meeting with Suzaku solidifies the evidence. In exchange for Japan's independence, the Black Knights agree to betray Lelouch. Unable to escape, Lelouch tells Kallen he was using her all along to keep her from sharing his fate, but whispers that she should live on within earshot. Lelouch is prepared to accept death, until Rolo, piloting the Shinkirō, rescues Lelouch and escapes the combined forces of the Black Knights and the Britannians. However, the excessive use of his Geass required to do so overtaxes his heart and dies after flying Lelouch to safety. Lelouch resolves to not waste the life given to him by Rolo, declaring he will kill the Emperor by his own hand.

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.