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Guys, either I'm a dick for not realising sooner, or I just figured something out.
In Pokemon: The Origins (Fuck you guys, I liked it), when Fuji is explaining the stones, he says something along the lines of "When a boy has a strong attachment to his Charizard" or something. It was something specific to do with Charizard though.
And I had a thought. Since Fuji was known to experiment a lot to make Pokemon 'More powerful', and he was talking specifically about Charizard, could the test subjects he used be Giovanni and his Charizard?
I mean, those tests could have been pretty changing, and it could have done something pretty bad. Maybe it's how Giovanni lost his Charizard, and maybe that is what turned him into a business tyrant who doesn't give two shits about Pokemon.
But yeah, I just kinda linked these two together, thoughts?