PokéBase - Pokémon Q&A
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This really bothers me because it was set in the Unova region, where Mega stones never existed yet. My only guess is it was one of those late movies where the Pokémon from that region somehow appeared only in another. Like how Magearna is in the Kalos region, but you can only get it in Alola.

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It mega evolves like how [email protected] and Rayquaza do in the hoopa movie
The games and the TV show are made by very different people. Don't expect them to be similar.

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Think about this though Mega Stones always existed. They're just not plentiful or existent in Unova. But Mewtwo isn't from Unova, It's from Kanto where mega stones do exist IE Mr.Fuji as well as Mewtwo appearing in different locations around the pkmn world that do have the stones IE Kalos Pkmn It's arbitrary to think that pkmn stay in one location there whole life and Mewtwo is the kinda pkmn to pick one of those up and you could argue for a human connection and thats how he does it. But I could seen him doing it alone (In the fkrst pkmn movke there was a scene that got cut which was mewtwo talking to a little girl while they were in the test tubes which means they clearly built a psychic connection which could be argued to why Mewtwo can go mega like that but I could see Mewtwo doing it himself its that type of pkmn. This is of course just a theory a strong one at that! But still just a theory. Hope I helped!

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