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So, where is Mewtwo and the other Legendary?
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Cover legendary, after you received your 7th badge: Just like Black and White, you actually NEED to catch it in order to advance the story (it won't let you progress unless you do and fainting it will result in no exp gained and it standing/floating there wanting to 'help' you)
As for the currently known post-game legendaries, here's a link: www.serebii.net/xy/legendary.shtml