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Arceus created several universes in his time, such as the Pokemon Conquest universe being one where Dark and Steel types were apparently already discovered, assuming that is isn't the same as the main universe either being back in time or in a pseudo-medieval stasis, how does this explain Mewtwo?
Maybe Arceus artificially created a Mewtwo of Conquest to see how it would react, basically like a Kid playing with a Toy T-Rex pretending to shoot Army Guys with mouth-launched missiles.
This theory also extends to Time-travel and parallel universes; one of which is the Dungeon universe which flows normally until the player of Time/Darkness saves the day, potentially causing a split timeline within that one, one of the potential eventualities lead into the Managate's time, he may have also experimented by destroying human worlds for no reason other than to possibly seed intelligence within the Mystery Dungeon universes via Human Agents.
He may have also kidnapped Pokemon such as Klink and Brozong/Bronzor to indirectly give human ideas, Klink being from a steampunk/Victorian universe...Klink being discovered 100 or so years ago..before the steel type and 5th gen Pokemon was discovered.
After living countless lives in billions of universes, Arceus nestles in Sinnoh to retire or possibly die, until the humans of that Universe got in its face, being caught in its frail state, arceus looped tons of times across timelines in tons of universes, the Unova one in gen 4 was it's "end", B/W also has 2 timelines.
The Prime universe is where Arceus got bored, and imbued Humanity with Pokemon-esque powers that would've looked out of place in a real world, such as Aura detection/emission and psychic powers.
