Depending on the level of your Mewtwo (which is likely 100, knowing what people do), and if you're on a new save game or not, it will disobey your orders and either:
* Have a nap, unless the Pokemon either has an ability or is under the effect of a move that prevents sleep
* Will cause confusion damage to itself
* Simply not attack
This is a mechanic put in place to prevent players from being traded high-level Pokemon from friends and blazing through the game with them. This also happens for artificially generated Pokemon (ie. through PKSM, PKHeX or similar means) unless you go through the effort of making the Pokemon look like it was caught in-game by you (ie. changing its OT Name, TID and SID values, though this may not be sufficient depending on the Mon)
Read more:
https://bulbapedia.bulbagarden.net/wiki/Obedience