In this enhanced remake of Pokémon Ruby Version, players travel throughout the Hoenn region on a journey to become a Pokémon Master. Like the original, the goal is to challenge the eight Pokémon Gyms of the Hoenn League and earn badges from their Gym Leaders, then take on the Elite Four and the Champion. However, the world is endangered when the villainous Team Magma tries to expand the continents by resurrecting the ancient Legendary Pokémon Groudon.

Aside from technical upgrades, the game is drastically changed in certain aspects. The Hoenn Pokédex is changed to add the evolutionary relatives of Pokémon from its original incarnation. Some Pokédex entries are also changed. Mega Evolution plays a major part of the storyline, and a new form change is introduced in the form of Primal Reversion, exclusive to Groudon and Kyogre. Some characters have had major redesigns in terms of appearance. Instead of roaming Hoenn after defeating the Champion as in the original, Latios automatically joins the player's party after summoning the player Southern Island. Latios can be used to soar through the skies of Hoenn, taking the player to locations known as Mirage Spots that cannot be reached otherwise. Pokémon Contests return under the name "Contest Spectacular" and have some new mechanics, while the basic format is largely the same.

After the main story, a new chapter called the Delta Episode is unlocked, allowing the player to once again save Hoenn from disaster. Finally, the Battle Tower is replaced by the Battle Resort, which features tough Trainers as well as a replica of the Battle Maison from Pokémon X and Y.