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It probably can't be natural, because Mewtwo is an artificial Pokemon, so how does Mega-Mewtwo exist?

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This more or so speculation, but considering Mewtwo was created after the Great Kalos War, Mewtwo Mega stone could be artifical. There's a "meme" on this.

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It probably is due to Mewtwo being an artificial Pokemon created by Team Rocket. But, it is unknown. If you have watched Pokemon Origins, Mr Fuji is possibly Professor Fuji and created the Mega Stones for Mewtwo, to make it not only the 'most powerful Pokemon' but also the 'most powerful Mega Evolution'. But, for the most part it is unknown.

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