But before Charles can confront God, he is himself confronted by Lelouch.
Lelouch has placed bombs at the entrance and seals both of them in the Sword.
Whatever Charles is up to, if he can't affect the world, he's as good as dead, even if he is technically immortal.
Here in this alternative world is the Collective Unconscious or God. Charles' plan is to remake the world so that individuals no longer exist. We are all just facets of the collective unconscious anyway.
Marianne, C.C., and V.V. were his allies in achieving this.