To capture Mewtwo in an Ultra Ball take at least 3 Ultra Balls with you to the Unknown Dungeon.(You must be a League champ first). Go find Mewtwo and Save the game before you assume battle mode with him. He is an icon that stands alone on a island. The icon looks just like Nidorino's icon and Snorlax's icon when they are in your list of 6 Pokemon. Enter the battle and have a Pokemon that is outfitted with the skills: Thunder Wave, Sleep powder, and Ice beam. Have a Pokemon at least at level 40. Do not worry Mewtwo is much, much stronger than you think. If Mewtwo is at level 100 he is more like your first PKMN at level 105. The thunder wave works best if you weaken him alot. After weakening him and Paralyzing him use an Ultra Ball. I don't think you needed 3 Ultra balls because when he is weak and paralyzed he is your's in one shot!!!