The storyline takes place two years after the chaotic events of Kyogre and Groudon's clash in Hoenn, with rumors spreading that the legendary trio has migrated to the Sierra Region. Consequently, Team Magma and Team Aqua arrive in Sierra to accomplish their respective goals of capturing Groudon and Kyogre. However, a brand-new organization called Team Empyrean emerges to stop them, aiming to capture Rayquaza first to prevent both syndicates from succeeding.