It is a Pokémon Team Magma stole that one of the Team Aqua's Admins, Shelly, disguised herself as a Team Magma Commander and gave Kyogre 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 Pikachu (possessed by the Blue Orb) awakened Groudon, Groudon tried to take out Kyogre. When it did, the Red Orb came out of Archie's chest and Kyogre was set free. But Archie fell out of his plane from the impact, after the Red Orb came out of his chest, fortunately for Archie, Lance's Dragonite caught him. But after the Blue Orb came out of Pikachu's body and fell into the water, Ash dove after Pikachu and saved it. Kyogre swam towards Ash and Pikachu when it looks as though if it was going to attack them. However, since Kyogre is no longer under the control of the red orb, it brought them to the surface instead. After both Legendary Pokémon are calmed down and the Orbs were destroyed, Kyogre went back to the sea.