About 100 years ago, There were two ancient behemoths who roam the Hoenn Region, constantly fighting in wars over the land and the ocean. These conflicts were so intense that a powerful deity must descend from the ozone to end the war of land and ocean. After the deity left Hoenn, The conflicts were finally laid to rest.
Years later, after the Pokemon League Champion, Wallace has been defeated by Norman's Child, May and the Hoenn Region has been living in peace, until two organizations were formed. Team Aqua, lead by Archie desires to summon Kyogre to control Hoenn's Oceans while Team Magma, lead by Maxie desires to summon Groudon to control Hoenn's landmasses.
Mephiles was a trainer born in the Kalos region who desires peace in all regions, so he travelled to Hoenn so he could start his Journey to put an end to Team Aqua and Team Magma's Plans for good with the help of May, Wallace, and Zinnia.
After Mephiles became the Champion of Hoenn, however, He would go on to push his agenda for world peace. After Team Aqua and Team Magma were disbanded, the former admins for both teams went and joined Mephiles, who had took over the Devon Corporation and formed Team Nameless from it.
A fledgling trainer, Wally decided to join Team Nameless to succeed Mephiles as the new Hoenn Champion. After the new organization was formed, The first course of action is conquest. In order to push this agenda for world peace, Team Nameless would start conquering other regions and their Pokemon Leagues by defeating the evil organizations and champions of those regions.