He either swallowed a Greninja or a bunch of crystals.
http://www.nintendoworldreport.com/news/41406/pokken-tournament-reveals-new-mewtwo-form
A Japanese livestream this evening of Pokkén Tournament has revealed a previously unknown form of Mewtwo.
The new form appears to challenge a Gengar following its defeat, and goes through a Mega Evolution ritual that causes large crystals to form on its back. It is not known whether the Mewtwo is exclusive to Pokkén or may appear in a future Pokemon game.
The battle can be viewed below:
