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 transfers into Ashford Academy and faces the scorn of the Britannian students. Cornelia continues her hunt for Zero, destroying several rebel strongholds but finding no clues to his whereabouts. A stray cat slips into the Lamperouge residence on campus and takes off with Lelouch's Zero mask and a massive, comedic chase involving the entire student body follow. The Emperor of Britannia makes a speech during Prince Clovis' funeral on the virtues of inequality and the social battle for evolution and betterment.

To Lelouch's surprise, C.C., the girl who gave him his power, is alive and now living in his residence. Suzaku, having been acquitted of all charges, accidentally meets Third Princess Euphemia li Britannia and ends up intervening in an internal Purist faction struggle. Meanwhile, Second Princess Cornelia li Britannia endeavors to take charge of Area 11 as Viceroy and bring Zero, now the Empire's number one enemy and most wanted man, to justice.

Told mostly from Kallen's perspective, her rocky relationship with her biological mother is revealed. The Black Knights are sent on a mission to take out the drug "Refrain", and find themselves to be popular among the Elevens. Kallen's mother is found among the Refrain users, and is arrested following the Black Knights' destruction of the drug stockpiles. Kallen promises to have changed the world by the time she is released.

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.

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.

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.

Lelouch confronts Clovis about the murder of his mother, Marianne vi Britannia, before killing him. When he returns to Ashford Academy, he discovers that Kallen Kōzuki, one of the terrorists he helped in Shinjuku, attends the same school. The limitations to his newfound power are also revealed to him when he attempts to question her then erase her memory, so he creates a cunning deception to ease her suspicions of his identity. When the death of Prince Clovis is announced in the media, it is Suzaku Kururugi who is accused of the murder.

The aftermath of the Avalon's arrival inexplicably leaves Lelouch, Euphemia, Kallen, and Suzaku on the island of Kaminejima. Suzaku encounters Kallen while Euphemia is found by Zero. Suzaku learns Kallen is a Black Knight and pilot of the Guren Mk-II, and in turn tells her about how he killed his father. Euphemia confirms her suspicions that Lelouch is Zero. Schneizel, Lloyd, and Cécile Croomy survey the island's ancient ruins. When Lelouch, Kallen, Suzaku, and Euphemia suddenly fall into the ruins, Lelouch and Kallen steal the prototype Knightmare Frame Gawain to escape. Elsewhere, the exiled Japanese government from seven years ago launches a full-scale assault on Kyūshū with the help of the Chinese Federation.

The Britannian Army fights back against the Kyūshū invaders with the Lancelot. Meanwhile, Nina meets Princess Euphemia and inadvertently gives Euphemia peace of mind about her feelings for Suzaku. As Suzaku becomes cornered when his Lancelot's battery runs out, Euphemia encourages Suzaku to fight on and live. Zero and C.C. fly into the battlefield in the Gawain to recharge the Lancelot, and the two Knightmares end the Kyūshū campaign together.

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.

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.

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.

Using his newfound power, Lelouch hijacks an enemy Sutherland and leads the rebels in a counterattack against the Britannian army, forcing Viceroy Clovis la Britannia to call for the release of an experimental Knightmare Frame, the Lancelot, piloted by Suzaku Kururugi. The Lancelot proves to be far superior to the previous Knightmare Frame models and Lelouch is forced to change his plans. Just as the Britannian Army corners the terrorists, Prince Clovis orders an immediate cease-fire, as he is being held at gunpoint by Lelouch.

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.

Cornelia and the Britannian Army heads to Narita, hoping to destroy the remnants of the Japan Liberation Front. Lelouch has his Knights follow her in the hope of capturing her alive so he can question her about his mother's death. As the Britannian forces close in on the Front's headquarters, Kallen utilizes her new Knightmare Frame, the Guren Mk-II, to cause a massive landslide that takes out much of the Britannian forces.

C.C. departs as a messenger to the Chinese Federation and Milly has a marriage interview with Lloyd Asplund, creator of the Lancelot. Mao returns to kidnap Lelouch's sister, Nunnally, and holds her hostage in the Ashford Academy sewers. Lelouch and Suzaku work together to rescue her, with Suzaku's physical adeptness and the clever use of Lelouch's Geass proving to be beyond Mao's planning. Before he can be arrested, Mao reveals that Suzaku killed his own father, and in return Lelouch silences him with his power. C.C. returns to the campus and finally ends Mao's life as Suzaku crumbles to the ground, confronted with his actions after years of secrecy.

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 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.

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.

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.