By the power of Aura...

After the horrific battle between the Dragon Titans in the Sinnoh region that lead to the ever powerful God of all Pokemon, Arceus, to be awoken, Mewtwo sensed the mighty Aura of the Original One, and sought to challenge such a being. It would question its own existence to Arceus, as a real Pokemon, or just a human experiment gone wrong. But Arceus refused to answer its questions, instead attacked the lone Mewtwo, causing a revelation that Mewtwo was in fact a creation of humans, but still a Pokemon. Thus, compressing its own Aura into itself, it forced itself into evolution, and proclaimed itself as "Mewtrix". Arceus was stunned at this, but not disaltered, as the Original One fled, presumably to another dimension, as Mewtrix failed to locate its Aura.
Mewtrix vowed to search for Arceus, and to force the answers out of the God, even if it meant destroying them both...

In the mainland of Torghan, the Peril Mountains are said to hold a mysterious connection with the Spear Pillar at Mt Coronet in Sinnoh.
A young trainer is suddenly awoken from their sleep in the middle of the night by an apparent earthquake
...Is it here?, the trainer hears...

~~~
Lawd, I've been wanting to do that FOR EVER!
Now, for a Mewtwo to force itself into evolution actually comes from Prinn-Dood's [link]
However, the idea of a Mewtwo simply 'evolving' as normal, ie maintaing the same structure and shape, really didn't sit well with me, so a more 'Aura advanced' evolution was needed. Sue me for idea theft, but it ain't

This idea has been sitting with me for quite some time, however, I hadn't really finished it until a few days ago, in which I editted colours, his right 'hand', and patterns. The extremely broad shoulder are NOT a sprite fault, as his 'black shoulders' are meant to be eliptical prisms, like a partial 3D oval. He's blended his memories of the Team Rocket cyber-suit that he wore in the first Movie, and accessed a deep recession of his own DNA that allowed to freely morph his body at will
"Mewtrix" comes from "Mew" and "Matrix"

As Mewtwo forced itself into evolution, you as a Trainer cannot evolve a Mewtwo in Mewtrix. Thus Mewtrix has to be caught, if possible in order to find its PokeDex data. But seeing as this is a non-natural evolution, its highly likely that there will ever be any data on it

btw
That story happens AFTER the events of the 12th movie, so if anything happens that contradicts this story (ie Arceus ends up back asleep), we won't count the movie as part of the 'game' series

Pokemon, "Arceus", "Mewtwo" (C) Nintendo, GAMEFREAK, etc
"Mewtrix" (C) Polursine