Kyogre and Groudon were summoned to ancient Dahara City by Hoopa one hundred years, before the time of Ash Ketchum, and were enraged by Hoopa's actions. Both tried to attack Hoopa, but Hoopa used its rings to redirect Groudon's attack towards Kyogre, cancelling out Kyogre's attack in the process. Both were then returned to their previous locations.
One hundred years later, Hoopa's dark side summoned Kyogre again, this time in its Primal Reversion form. Under Hoopa's control, it joined Giratina, Primal Groudon, Palkia, Kyurem, and Dialga in attacking Hoopa's nobler side and its friends. Upon the defeat of Hoopa Unbound, Kyogre was released and briefly collapsed from exhaustion. It then worked with its fellow Legendary Pokémon to try and save a number of humans and Pokémon from a time-space warp, and then departed for home.
- It has the ability to fly, which Kyogre cannot normally do.
- As with many of the movie Legendary Pokémon, it is unknown whether this Kyogre is the same that has appeared previously in such media as the Pokémon Anime, MS009: Pokémon Movie - Pokémon Ranger and the Temple of the Sea, or the Mega Evolution specials.