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.

During the commemoration ceremony for the Specially Administrated Zone, Lelouch and Euphemia privately discuss Japan's future. She convinces him, and Lelouch summarily halts his rebellion, until he suddenly loses control of his Geass while jokingly telling her to kill all the Japanese. The Geass-influenced Euphemia orders a bloody massacre of the people attending the ceremony. Blaming himself, a resolute Lelouch decides to salvage the situation by declaring Euphemia's Specially Administrated Zone a trap to lure out the Black Knights, and commands his troops to defeat the Britannian forces, protect the Japanese, and stop Euphemia.

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.

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.

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.

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.

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.

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.

Left with no choice, Lelouch shoots and mortally wounds Euphemia in front of Suzaku. Suzaku returns to the Avalon with her battered body as the Black Knights continue to contain the violence. She succumbs to her injuries as Lelouch announces his plan for the creation of the United State of Japan. Alone, Lelouch grieves over his actions as C.C. comforts him, reminding him that she will stay alongside him, as per their contract. Soon, the entirety of Area 11 revolts against the Britannian Empire. Advancing with his massive army, Lelouch ignites the conflict by initiating the collapse of the Tokyo Settlement.

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.

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.

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.

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.

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.

Lelouch's strategies give the Black Knights and their allies the upper hand in their battle against the Britannian Army. As riots break out through the country, the Black Knights take over the Ashford Academy as their headquarters, and the students are spared on Lelouch's orders. An enraged Suzaku, now informed of Zero's identity by a mysterious young boy named V.V., pursues Lelouch for revenge, which Cornelia also covets.

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.

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.

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.

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 Black Knights' assault on the Britannian Army in Narita proves successful, and Cornelia is cornered by Kallen and Lelouch. The army is pinned down by the Japan Liberation Front when they attempt to assist her. At Euphemia's request, Suzaku rushes onto the battlefield in the Lancelot to rescue Cornelia. He saves Cornelia and manages to corner Lelouch. C.C. comes to Lelouch's rescue by mentally traumatizing Suzaku, but is injured when Suzaku begins firing wildly. As he takes care of her, Lelouch inadvertently learns her real name. The Black Knights retreat from the conflict in victory, leaving the Japan Liberation Front and the Britannian Army to fight amongst themselves.

A group from the Japan Liberation Front takes a hotel and its occupants hostage, including most of the Ashford Student council and a disguised Princess Euphemia. As such, Princess Cornelia cannot make a move against the hostage takers, which Lelouch realizes and takes advantage of. He mounts a rescue with Ohgi's resistance, using his knowledge of Euphemia to barter his way past Cornelia's blockade. As Lelouch speaks with the hostage takers, Suzaku sinks the floating hotel using the Lancelot. Using explosives set up by the resistance fighters, Lelouch derails any rescue efforts by the army so he can take credit for their rescue. Broadcasting publicly to the nation, he announces the creation and purpose of his Order of the Black Knights, "allies of justice" who will judge the world and protect the weak from "those with power".

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.

Lelouch believes Shirley may have discovered his identity as Zero, so he and C.C. pursue her to Narita. Ohgi explores the battlefield of the previous night, discovering the wounded Villetta Nu left for dead out of sight. Lelouch encounters Mao, a young man who also has the power of Geass. Mao uses his mind-reading power to play on Shirley's insecurities, manipulating her into shooting Lelouch, but she falters at the last moment and C.C. sends Mao away temporarily. Since Shirley is being torn apart by grief and guilt, Lelouch uses his Geass to erase her memories of him.

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.

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.