Ein Jahr nach der Schwarzen Rebellion hat Lelouch Lamperouge sein normales Schulleben wieder aufgenommen, ohne sich an das vergangene Jahr zu erinnern. Nachdem er den Sportunterricht geschwänzt hat, macht er sich mit seinem jüngeren Bruder Rolo auf, um im Turm von Babel zu spielen. Angeführt von Urabe und C.C. startet der Orden der Schwarzen Ritter derweil einen Angriff, um Lelouch zurückzuholen.

Das Geheimnis der Verwandlung von Lelouch ist nun gelüftet! Der Turm von Babel hat sich in ein Schlachtfeld verwandelt. Ein mysteriöser Ritter erscheint dort vor den Schwarzen Rittern und ein erbitterter Kampf entbrennt. Die Schwarzen Ritter werden durch seine bedrohliche Kampfkraft in eine verzweifelte Lage gebracht.

Die verbliebenen Truppen des Schwarzen Ordens nutzten das Chaos im Turm von Babel und konnten entkommen. Der wiederbelebte Zero verkündet den Wiederaufbau der "Vereinigten Staaten von Japan"! Daraufhin kündigt das britannische Militär die Hinrichtung der wichtigsten gefangenen Ordensmitglieder an. Die Zeit wird knapp.

Aber Lelouch kann sich unter ihren wachsamen Augen nicht frei bewegen! In diesem Moment ergreift Lelouch eine unerwartete Maßnahme.

In seiner misslichen Lage bietet Lelouch Rolo einen Deal an.

Der Zeitpunkt der Hinrichtung rückt immer näher. Die Situation ist absolut ungünstig. Sein Erzfeind Guilford erwartet ihn. Und schließlich zeigt sich Zero selbst!

Die neue und größte Bedrohung: Kururugi Suzaku. Jetzt, als Ritter von Zebun, erscheint er erneut an der Akademie.

Inmitten dieser Spannungen schmeißt Mirei eine Willkommensparty.

Um den neuen Gouverneur des Gebiets 11 in ihre Gewalt zu bringen, starten die Schwarzen Ritter einen Überraschungsangriff im Pazifischen Ozean. Die luftgestützte Eskortflotte, die der wiederbelebte Zero unterschätzt, wird völlig überrumpelt. Die Operation scheint mit einem vollständigen Sieg der Ritter zu enden, bis der Nightmare Squadron aus dem Hinterhalt auftaucht. In dieses Getümmel stürzt sich der neu ausgerüstete Lancelot Conquestor. Und mitten in der großen Schlacht: Zero!

Lelouch geht ohne zu überlegen durch die Stadt, da er den Sinn des Kampfes aus den Augen verloren hat. Zur gleichen Zeit nähert sich Suzaku den Schwarzen Rittern, die in die Bucht von Tokio eingedrungen sind.

Der neue Generalgouverneur erklärt die Errichtung der "Administrativen Sonderzone Japan". Elfer empfinden dies allerdings als Schmach. Doch Zero unterstützt dieses Vorhaben, was den Schwarzen Orden verwirrt und man beginnt an seiner Loyalität zu zweifeln.

Britannia und der große Eunuch. Verarmte Untertanen der chinesischen Föderation. China ist in Aufruhr, als ob der blaue Himmel bereits tot wäre. Und das Schlachtfeld ist auch ... Mitten im Getümmel, wo Freund und Feind durcheinander geraten und sich die Kriegslage schlagartig ändert, zeigt der bedrohliche Albtraum "God Tiger", der schon zahlreiche Testpiloten verkrüppelt hat, endlich seine Zähne.

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.

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.

Having recovered her memories, Shirley questions her perception of reality. Lelouch heads to the train station to check on the delivery of a G Train, a network of Gefjun Disturber-equipped trains that will black out all of Tokyo once active. Meanwhile, Jeremiah makes his move on Ashford Academy, overwhelming Sayoko and Rolo in his search for Lelouch. Villetta willingly reveals Lelouch's location and Jeremiah corners him, but is paralyzed by the G Train. Struggling, Jeremiah asks why Lelouch betrayed the Emperor, to which the former prince reveals his motivation to avenge his mother. Having greatly admired Marianne, Jeremiah joins Lelouch's cause. Shirley finally reconciles her restored memories, asking Suzaku to forgive Lelouch as she has. Before she can reach Lelouch, she runs into Rolo, who uses his Geass once she reveals knowledge of Nunnally. As Lelouch leaves, he discovers Shirley mortally wounded, who confesses her feelings for him as he desperately commands her to live.

Rolo admits to causing Shirley's death; rather than blame Rolo, Lelouch blames the existence of Geass itself. In retaliation, he mounts an assault on the Geass Directorate, slaughtering every man, woman, and child within the stronghold. V.V. pilots the Siegfried in an effort to stop the Black Knights, but is defeated by both Lelouch and Cornelia. He escapes to the Thought Elevator, where Charles awaits, and when Lelouch follows he is transported to the Sword of Akasha. Meanwhile, Kallen and Nunnally discuss Lelouch. They are interupted by Suzaku, who, despite having been told that Shirley's death was a suicide, decides to interrogate Kallen using Refrain, in order to confirm his suspicion that Lelouch has become Zero again.

Suzaku realizes he cannot stoop to Lelouch's level to achieve his goals and decides not to use Refrain on Kallen. Instead, he heads to Ashford, where he discovers the Intelligence Agency is under Lelouch's control. Ohgi and Villetta meet in the woods, where Villetta intends to kill him, but Ohgi confesses that he has fallen in love with her. Sayoko interrupts and attempts to dispatch Villetta, and Ohgi is injured in the struggle. He tumbles off a cliff and Villetta jumps after him. Nina and the In Vogue staff make their first successful nuclear bomb test. Lelouch confronts the Emperor atop the Sword of Akasha. He learns the Emperor has taken V.V.'s "Code," which has made him immortal. C.C. appears and reveals to Lelouch her wish is to die, then transports him to "C's World" to ensure his safety, where he witnesses her past. Upon realizing her true wish, Lelouch returns to reality, proclaiming he shall be the only one to grant her wish. He attacks the Sword of Akasha with the Shinkirō and rescues C.C., only to find she has lost all her memories except those before receiving the power of Geass.

Forty-seven countries rally under the banner of the new United Federation of Nations, and their first declaration is to declare war on Britannia to liberate Japan. In anticipation, the Knights of Rounds and the bulk of Britannia's military force are transferred to Japan. Nina also asks to have the Lancelot equipped with her newly-developed F.L.E.I.J.A. (Field Limitary Effective Implosion Armament) bomb. The Emperor interrupts the Federation's announcement to challenge Zero to a battle for the world itself, since they are the only remaining powers in the world. Fearing for Nunnally's safety, Lelouch calls Suzaku and admits he's Zero, then begs Suzaku to rescue her. Suzaku agrees, but only on the condition that Lelouch meet him alone at the Kururugi Shrine.

The battle for Japan gets underway, and it does not start out well for the Black Knights. Luciano and Bismark decimate their ranks, with only Li Xingke to keep them at bay. Suzaku and Lelouch meet to discuss Nunnally. After some initial animosity, Lelouch manages to win Suzaku over. However, Schneizel has his personal guard arrest Lelouch, making Lelouch believe Suzaku has betrayed him. Schneizel and Lelouch have a private chat, and Lelouch is rescued by none other than Guilford, having used his Geass on Guilford beforehand to make him believe he is Cornelia. Using the Gefjun Disturber train network, Lelouch shuts down the Tokyo Settlement. At the same time, his reinforcements emerge from the ocean, ready to take advantage of the opportunity. Meanwhile, the Emperor is preparing for Ragnarök.

With the power disrupted, the Black Knights begin their assault on the Tokyo Settlement. Suzaku threatens to use the F.L.E.I.J.A. bomb, but Lelouch, having completely lost his trust in Suzaku, calls his bluff. Jeremiah and Guilford engage Suzaku, but Gino and Anya join the fray to even the odds. Sayoko frees Kallen while Rolo attempts to locate Nunnally, secretly intending to kill her. Lelouch is nearly killed by Luciano and his Valkyrie Squadron, until Kallen arrives in the upgraded Guren Seiten Eight Elements-Type. Meanwhile, the Emperor enters Area 11, and Cornelia escapes confinement. Using the new Knightmare's overwhelming speed and power, Kallen kills Luciano and severely cripples the Lancelot. On the verge of death, Suzaku's Geass command activates and compels him to fire the F.L.E.I.J.A. Unfortunately, the bomb detonates over the government complex, obliterating a massive section of the settlement. Lelouch has a nervous breakdown when Rolo tells him Nunnally is killed in the explosion.

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.

As the Emperor prepares to begin Ragnarok, Lelouch and Suzaku head to Kaminejima to face him. No longer restrained by his notions of wrong methods being meaningless, Suzaku strikes a deal with Schneizel to become the Knight of One, in exchange for assassinating the Emperor. Lelouch, using his Geass to its full potential, compels much of the Britannian military on the island to follow his commands. Meanwhile, the leaders of the Black Knights decide to declare Zero dead, as the truth will be far more difficult to swallow, but their story is doubted by others. Anya's mind is taken over by Marianne, who restores C.C.'s memories. The two begin to put their own plans into motion. At Kaminejima, Suzaku is held at bay by Bismarck, while Lelouch marches into the Sword of Akasha, through the Thought Elevator, unopposed. Knowing he cannot kill his father, Lelouch destroys the entrance, planning to seal them both inside for eternity.

Within the Sword of Akasha, Lelouch learns the truth about his mother's death from the Emperor and Marianne herself. The two reveal their intention to create a gentle world without lies, and begin Ragnarok. Lelouch almost reconciles with them, but changes his mind when he realizes that the world the Emperor desires has no future. Evolving his Geass to its next level, Lelouch defeats the Emperor with the help of the collective unconscious mind of every human, the personification of the "gods" the Emperor sought to defeat, dissolving both him and Marianne into dust. With Ragnarok ended, Lelouch takes up the throne as the new Emperor, using his Geass to make all the dissenters in the court acknowledge him as such. Suzaku is appointed as his new "Knight of Zero," while C.C. looks on from the shadows.

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.