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Let's say I battle Mewtwo in Cerulean Cave and it makes my entire team faint, sending me back to the Pokémon center.

Can I then go back into the cave and encounter Mewtwo again?

And is it the same for the legendary birds, and for remakes, Gen 2, etc?

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Yes, you only miss your chance if you knock it out, and only in the earlier games at that. Starting in BW2 I believe, any legendary you beat without catching respawns when you beat the Elite Four. But in all the games, you can challenge legendaries no matter how many times you lose to them.

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  • Bulbapedia says that the respawning on defeating the E4 started in Platinum, not B2W2.
    – jwodder
    Jan 3, 2021 at 3:36
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    What is your source for this answer? I don't actually know if whiting out causes Legendaries to disappear or not, but I do know that knocking them out isn't the only way to make them disappear. They also disappear if you run away from them, either manually, by moves, or with a Poke Doll (I tested these manually in game when I was younger).
    – BGamer
    Jan 3, 2021 at 7:43

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