Arceus, the god of Pokémon, finds himself threatened by a mysterious Entity that somehow usurped his power. In a last-ditch attempt to safeguard the world's fate, he calls upon the wish-granter Jirachi to summon a young human named Kyle, spiriting him away from his home in the human world and onto the Mysmor Islands - a vast land inhabited by Pokémon in a realm where humans don't exist.

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As the Entity's plot to seize the Pokémon realm unfolds, a zombie-like affliction starts assimilating the population. With his quest's perils and his own inhibitions mounting, Kyle learns he must somehow save the Mysmor Islands, lest the Entity ensure he won't have a home to return to.