Meta Rate My Team PokéBase - Pokémon Q&A
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I think someone already asked this question though.

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If you defeat the Pokemon League again, Mewtwo should come back. You could also do this if you defeated Zygarde.

Source: Experience

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No problem, but remove your answer and make it a comment. There's no need to thank me with an answer.
Don't ask and maybe he will.
If not, it's just a part of life here
I can get to 13k on BAs alone
Got a point Scraf
What do you mean DarkHeart? This info is perfectly legit.
I mean, there's a person guarding the entrance to the cave of mewtwo in pokemon village and unless you've already beaten the pokemon league u will not be allowed to enter
But maybe I'm wrong... It can even be that mewtwo appears after u beat the league the second time..