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Arceus created Rayquaza to keep Groudon and Kyogre in check, and Lati@s to help Ray do that. They both have a delta (Δ) on them - the symbol of Rayquaza.
Once every 1000 years or so, a large amount of meteors with powerful evolutionary material approaches the world, and each time either Rayquaza (with the belief of people causing it to mega evolve) or Arceus (as seen in the Arceus movie) destroy the meteorites, scattering mega stones, key stones and evolutionary stones across the world, constantly creating new species. They are somewhat hindered since Rayquaza eats a lot of them in order to maintain mega evolution.
Arceus created the world with such evolutionary material at its center, making pokemon able to evolve, and which is the primal power that Groudon and Kyogre are constantly seeking in order to undergo primal reversion and become powerful enough to reshape the world as they see fit.
When AZ's weapon was activated in XY, it hit the next bunch of meteorites, causing them to mutate, and creating Deoxys. Deoxys' many forms are because it is made from evolutionary matter - like a refined Ditto.
The fragments of Deoxys' meteorite will be responsible for the new pokemon found in generation 7+.
