Ruby and Sapphire

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 a small town called Littleroot Town. At the beginning of the games, the player chooses either Treecko, Torchic, or Mudkip to protect Professor Birch, the regional Professor, from an attacking wild Pokémon. After defending the Professor, the player is taken to his lab and receives the chosen Pokémon as his or her starter Pokémon. His or her friend, the protagonist's rival, is also a Pokémon Trainer and occasionally battles the player. The games' two main goals are defeating the eight Gym Leaders, proving oneself worthy of challenging the Elite Four and Champion to become the new Champion and completing the Pokédex by capturing, evolving, and trading to obtain all 202 Pokémon (It is possible to obtain all 386 Pokémon, but this requires trading with Pokémon FireRed and LeafGreen).

The most prominent subplot involves Team 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 and increase the region's landmass; in Sapphire, the Team Aqua are the villains and they try to use Groudon's counterpart, Kyogre, to increase the region's water levels. The player's father also introduces the player to Wally, a sickly young boy whom the player helps capture a Pokémon to be his companion as he moves away from the big city. Wally eventually overcomes his illness and becomes a successful Pokémon trainer, ultimately becoming the final challenger the player must face before the Elite Four.

Shortly before approaching the town of the first Gym Leader, the protagonist first encounters Team Magma/Aqua 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 Magma/Aqua. 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 Magma/Aqua 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 (the protagonist's father, the first time such a character appears), Magma/Aqua 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, Magma/Aqua steals an orb with the ability to control a legendary Pokémon (Groudon in Ruby, Kyogre in Sapphire). Magma/Aqua 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. Magma/Aqua, 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, but they have chosen the wrong one and have instead enraged the Pokémon instead of putting it under their thrall. 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.

Emerald

The setting and plot remains largely the same as Pokémon Ruby and Sapphire. Players can choose from either a boy or girl (resembling Brendan and May, both of whom have been given new outfits with a green color scheme, instead of the original red) and choose between one of three Pokémon before they proceed from their hometown into the rest of the game's world. Players are tasked with filling a device called a Pokédex by catching different Pokémon species and evolving them. They are also tasked to complete eight gym challenges and defeat the Elite Four and its champion by battling their Pokémon. Along their journey they face both Team Magma and Team Aqua (whereas Ruby and Sapphire had you face only one of them based on which version you had). Each has a goal to change the world to their liking; Magma desires more landmass while Aqua desires more water. They plan to accomplish their respective goals by summoning the legendary Pokémon Groudon and Kyogre. Late in the game, they both summon their respective legendary Pokémon; however the Pokémon refuse to obey either team and begin fighting, which puts the world in a constantly switching state of droughts and rain. The players' character climbs a tower in order to summon the legendary Pokémon Rayquaza, who quells the other two Pokémon's rage. After players beat the Elite Four, they are able to encounter two Pokémon flying across Hoenn called Latias and Latios and can access an area called the Battle Frontier.