It is a Pokémon Team Magma stole that one of the Team Aqua's Admins, Shelly, disguised herself as a Team Magma Commander gave Kyorge to Archie.
Archie took control of this Pokémon and used it to raise the water level so the world can be more friendly to Water-Type Pokémon. He flew above the Kyogre to control it. Team Magma was supposed to trade Groudon for Kyogre but Team Aqua went anyways to take this Pokémon. Archie first made it destroy Team Magma's Submarine. When Team Rocket let out Groudon, Groudon tried to take out Kyogre. When it did, the Red Orb came out of Archie's Chest and Kyogre was set free. From all the impact Archie fell out of his plane when the Red Orb came out of his chest. Shelly caught him when he fell, then Team Aqua escaped.
This same Pokémon appeared in Pokémon Ranger: Temple of the Sea (There is only one Kyogre known. So that would mean that Kyogre was NEVER truely caught, but was mind controlled by the Red Orb.).