Mewtwo is located at Western Cavern on the 99th floor. To unlock it, recruit all the Legendary Pokemon before him including Ho-Oh, Entei, Raikou, Suicune, Zapdos, Articuno, Moltres, Kyogre, and Groudon. In Western Cavern, you will be able to recruit almost all of the fully evolved forms of the nine starting Pokemon. To recruit Mewtwo you must defeat him with only one Pokemon in your team. When you get to floor 98, dismiss two of them and prepare for a battle. Mewtwo has around 900 HP.