This is pokemon mystery dungeron. There ARE no pokeballs in this at all.
Ok, to find Mewtwo in Dark Crater, I think you need to have Explorers of Darkness. He's not in Time. To add to that, you need the Mystery Part or Secret Slab in the bag when you get to the right floor. The floor is the Bottom 6th. When you get there, just look around and you'll find him eventually. He's pretty hard to recruit though. You can also check the list of pokemon on the floor by using the menu when you get there.
I advise having someone with the Fast Friend IQ, as well as holding the Amber Tear or Golden Mask, otherwise it'll be extremely hard to recruit Mewtwo.