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Inferences; Cipher was controlling Orre through the water treatment center in Phenac, which we know because after the operation is shut down (at the end of Colosseum), the ecosystem starts to recover, which you see in the sequel game, Gale of Darkness. Greenery starts sprouting back up, and wild Pokémon even return to the region.
And the second Cipher boss, Greevil, is the only trainer in any game to use seven Pokémon, four of which are legendary.
