This is my personal theory. It depends on the mon being a form or evolution and not Mewthree

Quite simply, Mewtwo is a member of the Mew family. The movie is called Extreme Speed Genesect! Mewtwo's Awakening!

Now hold up. Awakening. What could that mean?

Well, Mew can transform, yet Mewtwo, a member of the Mew family cannot

So perhaps after some deep reflection (Mewtwo gain power by remaining motionless in a sort of meditative state, according to the Pokedex), he reaches a sort of Pokenirvana state and changes into Newtwo

If permanent, then Mewtwo becomes the first evolving legendary

If temporary, then this form could, story line, last until the energy reserves are burnt through, returning Mewtwo to his normal state, ala Super Sonic to Sonic except he isn't fucked over by a stiff breeze