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We know that there are at least 3 universes:
The Mega Evolution universe featured in Gen VI and VII.
The non Mega Evolution universe featured from Ruby and Sapphire through Black 2 and White 2.
The OG Universe featured in the original Generation 1 and 2 games
This is why Pokémon Origins is different from what we played in Fire Red and Leaf Green, because it depicts the events as they occurred in the Mega Evolution universe instead of the non Mega Evolution universe that we played them in, just as Omega Ruby and Alpha Sapphire differ from Ruby and Sapphire.
