Lelouch pinpoints the cult of geass' headquarters and attacks with the black knights.
They kill the researchers and the experiments, some of whom are children.
Lelouch corners V.V., but a magic door opens and Charles is there, and Lelouch is pulled into a vision.
This is no mere vision. Lelouch is physically in the Thought Elevator/Sword of Akasha confronting Charles. He uses his geass and Charles shoots himself through the heart.
But it isn't that easy.
The final stage of geass is to absorb the progenitor's immortality.