PokéBase - Pokémon Q&A
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Well, people proboly want to know.

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Where did you get the idea that Mewtwo hates Mew? Is this to do with the anime?
It obviously has to do with Pokemon the first movie: Mewtwo Strikes Back
http://bulbapedia.bulbagarden.net/wiki/M01

1 Answer

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As we all know, scientists made Mewtwo as clone of mew. When Mewtwo found that he was not his own Pokemon, but as a copy of one, he sought to "destroy the original" as it seems.

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Mewtwo, you are your own Pokemon. You're special. :)
Oh. That makes more sense that what my friend told me. He said "Mewtwo hates Mew because he thinks one day he (Mew) will destroy him. Ok. thx
no probs.