Recent news has come out from Pokemon on how to obtain both of Mewtwo’s Megastones from X and Y!
For the other stones
Within the games, the other stones for the mega Pokemon are at the Battle Tree on Poni Island each costing 64 Battle Points (BP). This means you would have to battle (and win) 64 times just to get one stone, in total being 1024 battles!
For Mega Mewtwo X&Y
According to this tweet (and the associated link)
— Pokémon (@Pokemon) March 3, 2017
You can get the two stones through mystery gift by:
- Entering M2DECENT as the code in Mystery gift from the main screen
- Speaking to the deliveryman at any PokeCentre to receive the two stones
- Saving the game to secure your stones
The stones are not game exclusive unlike the two previous games but Mewtwo itself can’t be found in game, you will have to use PokeBank/Transporter to get him into the game from your previous games.
Hopefully this works for you and you start to use Mega Mewtwo X and Y more regularly (Even though its out of meta for competitive) but anyways.