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Mega Charizard X is the original Charizard from thousands of years ago, back when they spent most of their time in large caves in the mountains. The species ruled the caves and thus were able to populate more and more, to the point where the caves eventually became overpopulated and food within became scarce. They had to start leaving the caves more often to find food. As time went on, they had to fly further and further away to find sufficient amounts of nourishment, but their cave dragon wings weren't suitable for that kind of travel, so they had to adapt.
Their wings started to become more suitable for longer and faster flight, and thus they became part Flying type. They were also out in the sunlight more often, and thus turned orange and became what we know as Mega Charizard Y. As they spent less and less time in caves, Dragon type Pokemon like Haxorus and Druddigon started inhabiting the caves and eventually kicked the Charizard out for good.
As they started expanding their horizons, they came into contact with humans. Humans would eventually start catching and taming them. They adapted to a different lifestyle alongside the humans, and thus finally changed into the regular Charizard.
>tl;dr the Mega stones do not make them evolve further, but rather reverse their evolution to a time when they were more powerful than they are now.
