C.C. is introduced in the first episode, where she emerges from a fake gas capsule seized by Japanese rebels. She saves Lelouch Lamperouge from the Britannian soldiers trying to recapture her, taking the shot intended for him, and grants him the power of Geass on the condition that he grant her greatest wish. Lelouch accepts and is granted the power to control people's actions. Since she appears to have died following this, he leaves her body behind.

She unexpectedly reappears in the fifth episode, casually folding origami with Nunnally. From this point on she passively oversees Lelouch's missions as Zero, wanting to keep him alive so he can fulfill his contract, often going as far as wearing his clothes and impersonating him when situations become life-threatening.

When C.C.'s existence is revealed to the Black Knights, she gains considerable unofficial standing, as she is seen by other members to be one of Zero's closest advisers, if not his top adviser. However, her willful attitude and lack of an official posting annoys some veteran members and causes confusion as to her role within the Black Knights. At one point, Tamaki goes so far as to accuse her of being a member only because she's Zero's lover, a claim which she coldly denies. When the Black Knights gain possession of the Knightmare Frame Gawain, she becomes its pilot while Lelouch operates the weapons.

In the season finale, she uses the Gawain to battle Jeremiah Gottwald's Siegfried so Lelouch can save his sister. She drags both it and herself to the ocean floor to end the battle while narrating that the spark of Lelouch's actions was the core of human motivation: the desire for just a small amount of happiness. According to Yukana in a conference memo, C.C. was crushed by the water pressure, but being immortal, ultimately drifted to the surface and revived; it is stated that it was too gruesome to be shown.

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At the start of the second season, C.C. appears to be commanding the Black Knights. She and the rest of the surviving Black Knights initiate an operation to unlock Zero's memory that was sealed away by the Emperor of Britannia. Despite the Intelligence Agency having followed Lelouch in anticipation of that exact outcome, she is successful in restoring his memories. She takes up her old position following this.

She is revealed to have formerly led the Geass Directorate, a secret organization that studies and produces Geass users. V.V. succeeded C.C. as the leader, and relocated the headquarters to somewhere in the Chinese Federation. After pinpointing the location of the Geass Directorate, Lelouch orders C.C. to lead the attack against it. She reluctantly kills V.V.'s direct subordinates when they attempt to escape by bullet train in order to bury the existence of Geass. Her past is revealed to Lelouch after he is transported to the Sword of Akasha to face the Emperor. She also reveals that he would have become immortal had he granted her wish, which is to die, and spares him by offering her life to the Emperor. Lelouch refuses to let her die unhappy and rescues her, but she loses her memories of Geass and the related abilities, reverting to her personality as it was before she came under the contract that ultimately bestowed immortality upon her. Following her memory loss, C.C. remains in Lelouch's quarters, believing him to be her master.

When Lelouch's identity is revealed to the Black Knights and Rolo is forced to take him to safety, C.C. is left behind. Marianne, possessing Anya's body, locates C.C. and awakens her memories. The two then leave for Kaminejima, rescuing Suzaku along the way. Marianne enters the Sword of Akasha, while C.C. stays behind to spe