>>36285475Team Plasma also created Genesect, a very similar thing.
Also, in Episode Rainbow, Giovanni has a Mewtwo with a Megastone. We know Fuji had a Megastone in Origins, and Fuji was part of the group who created Mewtwo. I believe that Team Rocket probably made those Megastones artificially (ZardX too, why else would Zard get two, one so durastically different from the base form?)
So hypothetically, MewtwoX and ZardX are artificial creations from Team Rocket, then someone else somewhere (maybe Plasma, although I have doubts because Colress hadn't yet discovered Mega Evolution, they had Genesect instead) steals the idea and creates a second Mewtwo, and maybe the Y stone too, a more natural attempt at giving Mewtwo an evolution that makes it look more like a natural evolution of Mew, rather than just a powerhouse that was physically strong too like Rocket probably wanted.
Granted version differences muddy this as the wild Mewtwo and Giovanni's Mewtwo can both be found with alternate stones, but ehh.