The story takes place in the completely custom Tenjo Region, situated just east of Hoenn, where a mysterious crisis is unfolding: Pokémon are beginning to act strangely, with some going missing entirely while others refuse to obey their trainers. While regional scientists attribute the pandemic to a serious Pokémon virus, the player must embark on a journey to uncover the dark, underlying truth behind a corrupt government and an evil team seeking to exploit this phenomenon.