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 Purist faction within the Britannian Army scapegoats Suzaku for Clovis' death, planning to use him as an excuse to rid the army of Honorary Britannians. Lelouch concocts a plan to save his childhood friend, with some help from Kallen and Kaname Ohgi, leader of Kallen's resistance group. Announcing himself publicly as Zero, Lelouch declares it was he who killed Clovis, and uses his power on Jeremiah Gottwald to force him to assist in Suzaku's rescue. In private, Lelouch offers Suzaku the opportunity to turn against Britannia for falsely accusing him, but Suzaku refuses, wishing to change the Empire from within.

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.

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.

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.

Zero and the core members of the Black Knights meet with Taizō Kirihara, one of the most powerful people in the Japanese underground and an acquaintance of Lelouch from his younger days at the Kururugi Shrine. Lelouch deftly displays his tactical prowess and wit before Taizō and reveals his true identity to the man to gain his trust and support. When Lelouch returns to Tokyo, Shirley informs him of her father's death, indirectly caused by Zero during the Battle of Narita.

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.

C.C. explains her history with Mao, and how his inability to turn his Geass off drove him insane. An injured Villetta wakes up in Ohgi's apartment and he discovers she has selective amnesia. C.C. leaves Lelouch to take care of Mao herself, but Mao gains the upper hand when he incapacitates her. Lelouch utilizes his intellect to fool Mao and rescue C.C. from him, using the Britannian Police to surround and shoot Mao. Safe on a rooftop away from the scene, Lelouch affirms his contract with her, promising to not fall victim to his power as Mao did.

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.

An inauguration ceremony of Clovis' memorial art museum is being held, with Euphemia judging the art works. Lelouch agrees to help Kyoshiro Tohdoh's comrades rescue their leader and Shirley finds an old crumpled letter detailing her previous knowledge of Zero's identity. During the rescue mission, Lelouch convinces Tohdoh to join the Black Knights. The Lancelot appears and attempts to stop them, but Lelouch is able to predict its movements and plan a counterattack. When Tohdoh slices open the cockpit, revealing Suzaku within, Lelouch is shocked, having originally planned for Suzaku to become Nunnally's knight. He orders an immediate retreat as reinforcements arrive. Seeing Suzaku's bravery and creed, Euphemia announces to the media that he will be her knight.

As Euphemia knights Suzaku, Lelouch establishes the hierarchy of the Black Knights. Diethard Reid suggests assassinating Suzaku, but Lelouch has other plans for him. He launches a plan to disable and capture Suzaku and the Lancelot at a Britannia military base on Shikinejima. The plan almost succeeds, but Second Prince Schneizel el Britannia appears and orders his floating battleship, the Avalon, to bombard the island.