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V.V. was just a punk brat who seemed to think that he and Charles alone were better than the rest of the world and deserved to be above it. Kinda like Lelouch used to do with Nunnally though he eventually got over it. Marianne didn't fit into that equation obviously so she needed to be dealt with. Considering this is the same guy who gave Rolo his "The solution to every problem is to kill the source even if its only slightly possible to be a problem in the first place." mentality it's not too surprising.
I actually thought Charles and V.V. had some different plan at the beginning. But after his own brother selfishly murdered his wife and then tried to hide it(things they swore to fight against in the first place) that was the last straw for Charles who decided humanity really couldn't be changed on its own and decided to force drastic change on it through Ragnarok.
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