Mewtwo can be found in the Pokemon Village. Cross a small stream on the western side using the Surf HM to reach a cave entrance. Mewtwo will be inside immediately after entering the cave. At first, a man will block the cave entrance, but he will disappear once you defeat the Elite Four. Mewtwo is Level 70; use a Master Ball to easily capture him, otherwise it will be a long battle and require a lot of Ultra Balls. As soon as you capture him, you will also get the special stone needed to activate Mewtwo's Mega Evolution.