The setting and story of Omega Ruby and Alpha Sapphire are largely the same as the original Ruby and Sapphire games. They begin as the player is seen riding in the back of a moving truck. The player character starts by moving to the Hoenn region from the Johto region with their mother, as their father Norman has been hired as the leader of the Petalburg City Gym. The player arrives with their parents at the family's new home in the village of Littleroot Town, on the southern edge of the main island. The player character begins their Pokémon Trainer journey by saving Professor Birch, the leading scientist in the Hoenn region, from a wild Pokémon, choosing either Treecko, Torchic or Mudkip to defend him. Following the defeat of the wild Pokémon, the player receives the chosen Pokémon as their starter. They then travel around Hoenn to complete their Pokédex and battle the eight Gym Leaders of the Hoenn Pokémon League.
Along the way, the player character encounters the antagonist group Team Magma in Omega Ruby or Team Aqua in Alpha Sapphire who wish to use the power of the legendary Pokémon, Primal Groudon in Omega Ruby and Primal Kyogre in Alpha Sapphire, to change the world to suit their desires. Team Magma wants to use Groudon to dry up the oceans and expand the landmass, thereby allowing humanity to progress further, while Team Aqua wishes to summon Kyogre to flood the lands and revert the world to a prehistoric state, which will allow Pokémon to live more freely. However, unlike the original games, Archie and Maxie depending on the game version will actually use the correct orb, leading to their Primal Reversions. With the help of Hoenn League Champion Steven Stone and the Gym Leader Wallace, the player defeats their respective team and then either captures or defeats the legendary Pokémon to prevent a global drought / heavy rainfall and thus ensuring the teams' mutual reformation. The player then advances on to the Pokémon League, challenging the Elite Four and then the Champion, Steven, to become the new Hoenn Pokémon League Champion. The player also has the option of participating in the various Pokémon Contests throughout Hoenn, using their Pokémon to put on a performance for an audience and judges. Aside from the gameplay, 21 new Mega Evolutions were added since Pokémon X and Y, as well as "primal reversions" for Groudon and Kyogre, which function similarly.
