Charles has his own goals separate from VV dude.
You don't go that far without some ambition driving you. Charles: He didn't do it for the lulz.
He wanted to change the world too, and in the end he figured out that even with absolute power he cannot change the heart of a single person... even with fake memories and the false souls he puts in them.
So, he needs Lelouch to strip them of free will. His atonement is to make Lelouch take his place (and for him to kill off Schniezel, etc.)
In coming episodes:
More info on the situation regarding Marianne's fate. Turns out Schniezel wasn't really that bad of a guy after all. Battle for Tokyo happens after terrorist attacks, with chaos errupting everywhere. This time, things end differently. Britannia is driven from power and as Avalon is retreating it is blown up.
Spoilers suggest Lloyd dies, Schneizel probably also dies, Rolo dies, and Suzaku pays a terrible price for his betrayal.