You can only get Mewtwo after you have beaten the game. First go to Cerulean City and go past the five trainers. Take a left and you are in a grassy area. Then continue down the water (you need Surf to get in the water) until you see land. Get on that land and enter the dungeon (if you haven't finished the game, a guy will be blocking the entrance). Work yourself through the dungeon until you're on the bottom floor. You will see Mewtwo. Use your Master Ball to catch it.