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in the anime, ash knows mewtwo personally.In chapter 25 Chaletwo explains that Mewtwo was taken back in time by Chalenor and was still there when the War happened.
how is it possible, if according to the fic mewtwo died 999 years ago?
The number of times I get this question confuses me. Heck, it's even brought up again in chapter 39, so it's not as if it's just that single mention.