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If you make Mewtwo feint he will disappear from the cave. The way to get him back, as far as I know, is to go and beat the Elite 4 again upon which he'll return to the cave.

If you capture him, can you go repeat the Elite 4 and capture a second Mewtwo from the cave similar to how accidentally beating him will spawn another after the Elite 4 are beaten?

This would be particularly convenient for trading the X or Y Specific mega evolutions with a friend or family member who has the opposite game.

Edit: I guess this question could also pertain to other legendaries like Zygarde, Moltres, Zapdos & Articuono.

2 Answers 2

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No, once you have caught a legendary (that is able to respawn if beaten), it won't respawn again in the same game.

I believe this done to prevent having dozens of legendaries from the same game (in the sense you mentioned, i.e. trading one away, get another, trade it yet away, get yet another...), while at the same time, give players the possibility to catch them if they accidentally faint the legendary Pokémon.

Legendary birds don't respawn in XY. Mewtwo and Zygarde can, however.

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if you are worried about xerneas/yveltal i found online that you are pretty much forced to get the legendary mascot of the game. it should say: it seems xerneas/yveltal wants to help.About the other legendaries saving before battle is key success if you or the legendary loses exit the game re-enter you should be at the legendary pokémon i did this with zygarde better that battling the league again hope this helps.

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  • @jerry is right about legendary birds
    – superdude
    Commented Nov 29, 2014 at 22:19

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