I can just imagine it now:
Lelouch confronts the cult and secretly arranges to be given the same immortality C.C. has without her, nor anyone else knowing.
Later at the end of the show, after he has destroyed Britannia and killed his father. He comments to himself "now there is only one enemy left." He meets C.C. shortly after, and she betrays him by robbing him of his Geass and shooting him through the heart.
A horrified group of Black Knights comes upon the two of them and angrily question C.C. who claims that Lelouch was killed and that she killed the Emperor for him. She demands that she be the new leader of the Black Knights and the ruler of the new world.
Halfway through the conversation the group of Black Knights stops talking and just stares at a spot behind C.C.. Two footsteps can be heard as Lelouch slowly rises from his place on the floor, and as C.C. turns around he laughs the most cruel, mirth-filled evil laugh he has ever laughed as the cult symbol glows on his forehead and he regains his Geass.