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Has Gamefreak told us how we are going to get
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in attempt to make pokemon more beautiful and fabulous team flare is trying to force mega evolutions however true mega evolution is only supposed to happen with pokes that relay like their trainer or something
somehow using xerneas/yvetal (depending on version) they are able to manipulate a forced mega evolution on some random pokes including mewtwo who you probably battle but can't catch until postgame where it's in like a cave or something