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.