Our story begins 30 or so years after the climactic battle between Kyogre and Groudon in the lands of Hoenn. Hoenn has slowly been declining over the 30 years, thanks to the intensity of the battle that the legendary pokemon had. The region of Hoenn has undergone a terrible terraform, as a result, that has caused the plants and Pokemon stress. For a while, the gym leaders were all around the region, helping to fix Kyogre and Groudon's work, but over time, the efforts were for naught. The land is still somewhat bare, and now there are strange people in dark garbs offering salvation.

We don't know who these people are, but they only speak the word, 'Shroud'. They have also been reported to be looking for gym leaders, for some reason. As a result of this, almost every gym leader back in those days has disappeared, seemingly off the face of the planet.

Our story begins in New Mauville, the safest haven among the entire region, the gym leader Wattson's technology keeping his people safe and allowing the people to live so long. He now runs his gym in New Mauville and trains the kids here so he can find an heir to the gym.