Pokémon Ruby and Sapphire Versions/Plot

The player starts their journey in Littleroot Town, where the family has just moved from the Johto region after the player's father, Norman, became the leader of the Petalburg Gym. The story starts off with the player riding in the moving van, which arrives in Littleroot. After exiting the van, the player's mother explains that they have just arrived at their new home; they then enter the house together, and there are movers carrying boxes. The player's mother suggests that the player introduce themselves to Professor Birch, a friend of Norman's.

Upon arriving at Birch's house, his wife greets the player, and upstairs the player meets or  (whichever is the opposite gender as the player), the child of Professor Birch who will become one of the player's rivals. After the introduction, Brendan or May soon leaves to join Birch, who is out in the field. The player then finds Birch on, where he is being chased by a. Birch asks the player to take a Poké Ball out of his bag, which is lying on the ground; the player then chooses between, , and as their starter Pokémon. After choosing, a battle immediately begins with the wild Poochyena. After rescuing Birch, he lets the player keep the chosen Pokémon as thanks for saving him. He then tells the player to meet up with his kid on for pointers on how to be a Trainer.

Once the player finds Brendan or May on Route 103, they have their first, after which they return to Birch's lab, where the player receives a Pokédex and some Poké Balls. Outside of the lab, the player's mother gives them the Running Shoes. Once the player arrives in Petalburg City, they meet with their father at the Gym, where he tells them that he is happy to learn that they have become a Trainer like him. During the conversation, a local boy named Wally enters the Gym and asks Norman to help him catch a Pokémon. Norman loans Wally a and a Poké Ball. He then asks the player to go along and help Wally with his task. On, Wally catches a , and the Trainers then return to the Gym, where Wally gives his thanks before being called home by his mother. Norman then encourages the player to travel Hoenn and challenge the region's Gym Leaders: Roxanne, Brawly, Wattson, Flannery, Norman, Winona, Tate and Liza, and Wallace.

The player then travels through and Petalburg Woods; just before the exit from the woods, the player encounters the nefarious Team Magma or Team Aqua. After battling, the grunt reveals that their team is after something in Rustboro City.

At the Rustboro Gym, the player battles Roxanne and earns the ; afterwards, the player runs into the Devon Researcher from Petalburg Woods. He tells the player that he has been robbed by Team Magma/Team Aqua and that the player must get the Devon Goods back from the evil team. The player then heads out onto and discovers an old man named Mr. Briney who tells them that the villainous team has also taken his  Peeko hostage and gone into the Rusturf Tunnel. The player confronts the grunt inside the tunnel and retrieves the Devon Goods, as well as rescuing Peeko.

Once the Devon Goods are returned, the researcher asks the player to deliver them to the shipyard in Slateport City. The player then meets Mr. Stone, the president of the Devon Corporation, who asks that the player stop by Dewford Town and deliver a letter to his son ; as thanks for the player's earlier work, Mr. Stone gives the player a PokéNav. Outside, the player meets Brendan or May, who explains that Mr. Briney had formerly been a sailor. The player then heads back through the Petalburg Woods to Mr. Briney's house, where he gives the player a ride down to Dewford Town. Just north of Dewford on is the Granite Cave where Steven is exploring. The player obtains at the entrance, but it will not work without the Dewford Gym's Badge. After earning the from Brawly, the player can now use Flash to find Steven in the Granite Cave and deliver the letter. Steven rewards the player with and tells the player that he/she could potentially become the Pokémon League Champion.

After leaving Dewford Town, Mr. Briney takes the player across and  to, just south of Slateport City. When the player arrives in Slateport, there is a noticeable crowd of Team Magma/Team Aqua grunts blocking the entrance to the Oceanic Museum. When the player tries to drop off the Devon Goods at Stern's Shipyard, they learn that Captain Stern is in the Oceanic Museum. Once the player finds Captain Stern, they are confronted by two villainous grunts, and after defeating them, the villainous team's leader Maxie/Archie appears and tells the player of their plans before warning not to get in the way again.

After giving the Devon Goods to Captain Stern, the player leaves Slateport City and travels ; after encountering and battling Brendan or May, the player arrives in Mauville City. Outside of the Mauville Gym, the player finds Wally and his uncle; Wally challenges the player to a battle to prove to his uncle that he is ready for the Gym. After the battle, Wally's uncle invites the player to visit Verdanturf Town sometime. Once the has been earned from Wattson, the player heads to Verdanturf Town and uses  to clear the previously blocked Rusturf Tunnel, earning  as a reward. Next, the player returns to Mauville and travels through and  to the Fiery Path, on the other side of which the player continues through  to Fallarbor Town.

Inside the Fallarbor Pokémon Center, the player meets Lanette, who invites them to her house on. At the end of Route 114 is Meteor Falls, where the player finds Team Magma/Team Aqua, who have stolen a valuable Meteorite from Professor Cozmo. Suddenly, the scene is interrupted by the appearance of the opposite-version's team, which causes the thieves to retreat to Mt. Chimney with the stolen meteorite. At the top of Mt. Chimney, Team Magma and Team Aqua can be found fighting; after fighting the male admin of the primary evil team (Tabitha in Ruby, Matt in Sapphire), the player finds the leader of the team using the meteorite in a strange machine. The leader then battles the player.

Taking the southern path that was blocked by the battling teams, the player exits Mt. Chimney and reaches Lavaridge Town, home of the Lavaridge Gym. After receiving the from Flannery, the player then meets Brendan or May, who gives them the Go-Goggles and suggests that they challenge their father at the Petalburg Gym. After getting the from Norman, the player visits Wally's father, who gives the player.

As the player then travels through (just east of Mauville City), they encounter Steven once again. Afterwards, the player continues through, reaching the Weather Institute, which is being attacked by the evil team in search of the that the institute has created. After battling the grunts and facing off with the female admin (Courtney in Ruby, Shelly in Sapphire), the player saves the institute and is given the Pokémon as a reward. Shortly after leaving the Institute, Brendan or May appears, battles the player, and gives away upon defeat.

The player arrives in Fortree City but cannot challenge the Gym because something invisible is blocking the entrance. On, the player once again meets Steven, and he gives the player the Devon Scope, which allows them to enter the Gym by revealing the invisible thing to be the Pokémon. After the player defeats Winona and receives the, the quest continues through and  to Lilycove City. On, there are some grunts from the evil team discussing their plan to go to Mt. Pyre, and upon arriving in Lilycove, the player finds it crawling with more grunts. Outside of the Lilycove Department Store, the player battles Brendan or May for the last time, who upon defeat announces his or her intention to return to Littleroot.

After the battle, the player heads to Mt. Pyre to drive off the evil team. At the summit of Mt. Pyre, the player finds the leader of the team, who has taken the Blue Orb/Red Orb and proclaims that the young Trainer has arrived too late to stop him; the team then heads for Slateport City. The old couple that watch over the orbs beseech the player to stop the evil team, and they give the player the stolen orb's counterpart. Upon returning to Slateport, the player finds that Capt. Stern has discovered an undersea cavern on. The evil team then suddenly appears and takes over the captain's research submarine. The leader of the evil team once again taunts the player, and he mentions that the team's hideout is in Lilycove City. Once the player fights their way through to the center of the hideout, finding the Master Ball along the way, they encounter the male admin who battles the player to stall until the leader takes off in the submarine.

The player must then travel to Mossdeep City. Steven's house is at the northwestern edge of the city, and here the player receives. Next, the player challenges Tate and Liza of the Mossdeep Gym to earn the. Heading to and using Dive, the player finds the Seafloor Cavern, where the evil team has gone. In the deepest reaches of the cavern, the player has a showdown with the team leader, who then uses the Orb to awaken the sleeping / there. After being awakened, the ancient Pokémon vanishes, and the weather all over Hoenn goes out of control. Just then, the leader of the opposite team appears, and the leader of the primary evil team finds that he is unable to control the Pokémon. The two bosses then team up to try to stop the rampage.

After the bosses leave, Steven appears and tells the player to head to Sootopolis City, to which Groudon/Kyogre has gone. Heading to and using Dive again, the player finds the entrance to Sootopolis City. Inside the city, the player finds Steven, who introduces them to his friend Wallace, the Sootopolis Gym Leader, who is also entrusted with the duty of protecting the Cave of Origin. Upon seeing the Orb that the player possesses, Wallace grants them entrance to the cave, where the rampaging ancient Pokémon is waiting. After capturing or defeating the Pokémon, the weather returns back to normal.

Afterwards, Steven is found waiting outside of the Sootopolis Gym to thank the player on his and Wallace's behalf before the player faces the final Gym challenge. After defeating the Gym and leaving with the in tow, the player now has all eight Badges, and they head down  to Ever Grande City, where  and the Elite Four await. Wally battles the player one last time before they exit the cavern.

The Elite Four are the strongest Trainers in the region, and they can only be battled by challengers who have all eight Badges of Hoenn. They are Sidney, who specializes in Pokémon; Phoebe, who specializes in  Pokémon; Glacia, who specializes in  Pokémon; and Drake, who specializes in  Pokémon. After defeating the Elite Four, the player must then battle the Pokémon League Champion, Steven.

After the battle, Professor Birch and Brendan or May arrive to congratulate the player. Birch examines the player's Pokédex, the player is registered in the Hall of Fame, and the credits roll.

After the credits, the player is returned to Littleroot Town. Downstairs, Norman gives the player the S.S. Ticket to take the S.S. Tidal over to the. The player also now has the ability to encounter at the Sky Pillar and find /  around Hoenn.