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.

Lelouch returns to the Ashford Academy during the broadcast, causing Villeta Nu's Special Division to have doubts he was the Zero on television. Needing information on his sister's whereabouts, Lelouch sets a trap to turn Rolo into his pawn. Gilbert G.P. Guilford, Cornelia li Britannia's knight and acting Viceroy of Area 11, presents an ultimatum to Zero: reveal himself or let the incarcerated Black Knights face execution. Elsewhere, Suzaku leads the Britannian frontlines in the Lancelot in the war against the Euro Universe. Lelouch confronts Rolo, but Rolo's unique abilities allow him to gain the upper hand.

Lelouch deduces the nature of Rolo's Geass and convinces Rolo to spare him; in return, he will hand over C.C. Li Xingke confronts the Eunuch Gao Hai and kills him to take command of the consulate. As the deadline approaches, Guilford prepares to execute the captured Black Knights, until Zero appears, challenging him to a duel. Using the same strategy from the Black Rebellion, he collapses the portion of the settlement they are standing on, causing confusion amongst the Britannian military as they are dumped into Chinese territory. While Kallen and the Black Knights rescue the prisoners, Rolo appears in the Vincent to kill Lelouch for his betrayal. However, Lelouch takes a bullet meant for Rolo, giving the youth pause. Lelouch plays on his insecurities about his future and sibling relationship, convincing him to join his cause.

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.

Rolo uses his Geass to buy Lelouch time to say words of caution to Nunnally without revealing his reawakened memories to Suzaku. Unwilling to fight against Nunnally, Lelouch orders the Black Knights to capture her as she is transported to Area 11 by airship. Successfully boarding the vessel, Zero meets with her and tries to convince that Britannia is using her. Nunnally reveals she volunteered for the position, and states she wishes to continue Euphemia's Specially Administrated Zone of Japan, requesting a bewildered Zero to join her. Britannian reinforcements hinder the Black Knights' assault, and as the airship crashes into the sea, Suzaku manages to save Nunnally, taking her away from Lelouch a second time.

Nunnally is sworn in as the new Viceroy of Area 11, and reveals her intention to restore the Specially Administrated Zone of Japan. Knowing he cannot go against his sister's wishes, Lelouch slips into a state of depression. Before he relinquishes himself to Refrain, Kallen steps in, reminding him his duty as Zero to realize the dream he gave to the Japanese. An evesdropping Rolo emerges, attempting to persuade Lelouch to abandon his identity as Zero and return to being a high school student. Meanwhile, the Black Knights are under attack by a Britannian naval fleet, led by Suzaku. A glimmer of hope is revealed to Lelouch after he sees fireworks setting off at Ashford Academy. Rushing to the battlefield, he successfully leads the Black Knights to defeat the entire naval fleet and surprise Suzaku by appearing as Zero, announcing his intention to accept Nunnally's offer to join the Specially Administrated Zone of Japan.

The Black Knights question Lelouch's decision, and the Britannian Army remains wary of his intentions. In a private conversation with Suzaku, Gino Weinberg, Anya Alstreim, Lloyd Apslund, Cécile Croomy, and Miss Romeyer, Zero requests he be exiled from Area 11 in exchange for delivering one million participants. The Britannians think he is abandoning them to ensure his own safety, and accept. At the opening ceremony, Zero asks Suzaku what it means to be Japanese, to which the Knight of Seven replies it is a shared heart. When every participating Eleven dresses as Zero on cue, Suzaku has no choice but to exile all one million "Zeroes", unwilling to start another massacre in the face of their peaceful resistance.

Lelouch learns that the Chinese Empress Tianzi is being forced into a political marriage to First Prince Odysseus u Britannia. The wedding is orchestrated by the High Eunuchs, who will become nobility in Britannia in exchange for turning over half their land to Second Prince Schneizel el Britannia. As the wedding begins, Li Xingke initiates a coup-d'état to overthrow the Eunuchs, but before he can free the Empress, Lelouch appears and takes her hostage. Elsewhere, V.V. prepares to unleash Jeremiah Gottwald against Lelouch and C.C.

Lelouch successfully escapes with Empress Tianzi and the Black Knights attempt to unite with their Indian allies. Desperate to recover the Empress, the Eunuchs agree to forgive Li Xingke if he rescues her. To that end, he is granted use of the powerful Shenhu. Kallen intercepts him with the Guren Flight-Enabled Version, but its power runs out and she is taken hostage. Lelouch swears to rescue her, despite Diethard Reid's suggestion to retreat. Xingke demonstrates his skill as a strategist, forcing the Black Knights to retreat to a mountainside monument constructed as the tomb for the former Tianzi, hoping the Federation would be hesitant to attack. The Eunuchs turn on Xingke and his troops, having enlisted the aid of the Britannian forces. Meanwhile, another Lelouch is present at the Ashford Academy.

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.