Altera is a wild and diverse region that overflows with abundance as well as danger. It is also the only place in the Pokémon world that emanates large amounts of Flux energy, a potent resource that has many uses. The value and power of this resource led to rapid economic growth of the region. However, shortly after humans began tapping into Flux energy for power, reports started to emerge about vicious, powered-up Pokémon appearing: the Alter Pokémon.

To combat the new Alter Pokémon and preserve peace and prosperity in Altera, the Altera Pokémon League was formed. The purpose of this League is to produce strong trainers to fight the Alter Pokémon, rewarding them with money and fame. This prominent league attracts trainers from all over the world and is structured differently from a typical Gym challenge. After a championship match in Condor City, while going home, three friends meet face by face with the Alter Pokémon threat and soon after embark on a life changing journey across the Altera Region!