The demo has been confirmed to be just a showcase. Nothing in it actually happens in the game.
That said, how/when do you think you'll find Mewtwo in the actual game?
I'm guessing after you defeat the elite 4 you'll encounter postgame content where you'll find out that someone recovered cell samples from the original mewtwo and made a perfect clone of him. Of course it will escape again and you'll have to track it down to keep it from causing problems.
After you beat the Elite 4 and sail around some islands and crap establishing a Hoenn Link, you fly back to the town of the second gym leader and go through some huge-ass cave and find it at the very end.
Build a man a fire, keep him warm for a day. Set a man on fire, keep him warm for the rest of his life.