Code Geass C.C. in Second Season

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 by the kiss. She takes up her old position following this.

After pinpointing the location of the Geass Order, 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, apologizing for leaving them to their own devices. C.C. later reveals her wish to Lelouch after he is transported to the Sword of Akasha to face the Emperor, explaining that her greatest wish is to die and as Lelouch is not ready, she is offering it to Charles. Lelouch tells her she shouldn't die looking unhappy, promising he will make her smile while saving her. However, in the attempt, C.C.'s memories of everything past the day she acquired her Geass are lost, reverting her to a frightened slave girl. Believing himself to be responsible, Lelouch confines C.C. to his quarters and attempts to make her comfortable.

After Lelouch's identity is exposed to the Black Knights and he evacuated by Rolo, Marianne takes over Anya's body and uses it to locate C.C. and restore her memories. The two then leave for Kamine Island, rescuing Suzaku along the way. Marianne enters the Sword of Akasha, while C.C. stays behind to speak with Suzaku. She compares herself to him, as both have a death wish they cannot fulfill. Suzaku denies this and has C.C. take them to the Sword of Akasha. C.C.'s presence allows the Emperor to begin the Ragnarök Connection. When Lelouch turns the tables and the collective unconsciousness destroys Charles and Marianne, C.C. is spared their fate because she has turned against their plan.

Later on, after Lelouch seizes the Britannian throne, C.C. comforts him when he is troubled on what to do about Nunnally being aligned against him. Before heading into battle, C.C. asks Lelouch if he hates her for giving him Geass and changing his fate. Lelouch explains that he's grateful, both to Geass and her, for allowing him to move forward. She smiles and says this is the first time she's ever met a man like him. Lelouch says her name and the begin walking toward each other. They are interrupted when Kallen attacks in the Guren, ready to kill Lelouch. C.C. intervenes in her Lancelot, buying Lelouch time to escape, telling him to come back so he can make her smile. She engages in battle against Kallen. During their battle, Kallen questions her lack of motivation, and asks if C.C. loves Lelouch. C.C. isn't sure about the latter, still wanting to put an end to her unending life. C.C. is easily defeated, but ejects to safety, surprised that she even cares about winning or losing. During Lelouch's planned assassination, she prays for him at a church, shedding a single tear while commenting on the price he's paying for using Geass on others.

During the epilogue, C.C. is seen traveling the countryside in the back of a cart. She talks about how the Geass is supposed to bring loneliness, yet Lelouch proved this wrong. With the knowledge that Lelouch did not hate her for giving him the Geass, she is now able to express her true feelings addressing Lelouch, leaving his fate somewhat ambiguous.