We have two major universes now: a Mega Evolution universe and a non-Mega Evolution universe.Can someone explain to me this multiverse theory that is going around. I finished the story, so I must have just skipped over the text, and now I'm completely out of the loop. Is Gen III/Hoenn now the beginning of the canon or something?
Games from generations 1 to 5 take place in the non-Mega Evolution universe. There, AZ's war never happened, the weapon was never activated and as a result, Mega Stones and Mega Evolution never came to be.
Generation 6 games, so - Pokemon XY and ORAS, take place in a whole separate universe where AZ's war did happen (as explained in XY) and therefore Mega Evo exists there.