Pokémon Ruby and Sapphire take place in Hoenn, a fictional region based on the island of Kyūshū in Japan. The region contains nine cities and six towns along with different geographical locations, all of which are connected by Routes. As in previous games, some areas are only accessible once the player fulfills a certain condition.
Like other Pokémon games, Ruby and Sapphire's gameplay is linear; the main events occur in a fixed order. The protagonist of Pokémon Ruby and Sapphire is a child who has recently moved to Littleroot Town. At the beginning of the games, the player chooses either Treecko, Torchic, or Mudkip as his or her starter Pokémon from Professor Birch. His child, the protagonist's rival, is also aPokémon Trainer and occasionally battles the player. The games' two main goals are defeating the Elite Four to become the new Champion and completing the Pokédex by capturing, evolving, and trading to obtain all 386 Pokémon.
In addition to the main quest of defeating the Gym Leaders, there are side quests in which the player can aid NPCs by fulfilling tasks (usually obtaining items); other side quests involve catching legendary Pokémon. The most prominent subplot involves Teams Aqua and Team Magma, crime syndicates who want to use Pokémon to alter the climate of Hoenn. In Ruby, the villains, Team Magma, want to use the legendary Pokémon Groudon to dry up the oceans of Hoenn; in Sapphire, the Team Aqua are the villains and they try to use Groudon's counterpart, Kyogre, to flood the region.
Shortly before approaching the town of the first Gym Leader, the protagonist first encounters the Team Aqua/Magma in the Petalburg Woods, where he or she rescues a worker from Devon (a company that manufactures Pokéballs) and recovers Devon merchandise. Upon arriving in Fallarbor Town (after defeating the third Gym Leader), the protagonist discovers that Professor Cozmo, an astronomer, has been kidnapped by Aqua/Magma. The protagonist traces them to a cave, Meteor Falls, but is too late to stop them from escaping to Mt. Chimney with a meteorite. The protagonist follows Aqua/Magma to Mt. Chimney where they are preparing to use the meteorite to alter the climate of the region. The protagonist defeats the Team's leader, however, and returns the meteorite to Professor Cozmo. Shortly after the protagonist defeats the fifth Gym Leader, Aqua/Magma again attempts to change the region's climate by stealing a Castform, a Pokémon with the ability to change the weather, from the Weather Institute. After the protagonist defeats the sixth Gym Leader, Aqua/Magma steals an orb with the ability to control a legendary Pokémon (Groudon in Ruby, Kyogre in Sapphire). Aqua/Magma then steals a submarine from Captain Stern in Slateport City; the protagonist, however, infiltrates the team's hideout, but fails to prevent the submarine from being used. Aqua/Magma, then travel with the orb to the Seafloor Cavern, where Groudon or Kyogre resides; the team then uses the orb to awaken the legendary Pokémon. Once awakened, the Pokémon travels to the Cave of Origin and causes a region-wide drought (Ruby) or severe rainstorms (Sapphire). When the protagonist defeats (or captures) the Pokémon, the region's weather returns to normal.