In Pokémon Sapphire, Team Aqua will steal the Red Orb from the summit of Mt. Pyre and use it to awaken Kyogre. However, as Team Aqua have the incorrect orb, they cannot use it to control the super-ancient Pokémon as they intended. After Kyogre is captured or defeated by the player, he or she can return to the summit of Mt. Pyre to watch the Team Aqua Leader Archie return the orb to its proper place. Afterwards, the player returns the orb, and Archie departs. Team Aqua are not seen again after this.
In Pokémon Emerald, the same events that happened in Ruby and Sapphire take place, only both Team Magma and Team Aqua appear and therefore both the Blue Orb and the Red Orb are stolen. However, the player does not obtain the Red Orb.
The Red Orb was first mentioned in A Three Team Scheme!, where Shelly revealed that she was in possession of it. However, the dub incorrectly referred to the item as the Rose Orb in this episode.
The Red Orb debuted in Gaining Groudon, where it was shown to be under the possession of Archie, using it to control Kyogre after Shelly freed it from Team Magma's imprisonment. In The Scuffle of Legends, the Red Orb's influence caused Archie to send Kyogre on a rampage, threatening to drown even the members of his own team. As the Orb's influence grew, it was eventually absorbed into Archie's body. After Groudon had managed to defeat Kyogre, the Red Orb extracted itself from Archie's body, and was shortly afterwards destroyed, along with the Blue Orb.
In the manga
The Red and Blue Orbs in the Pokémon Adventures manga
Later, Ruby and Sapphire faced Maxie and Archie in a battle, but had difficulty in reaching them. After Ruby's Fofo finally managed defeat the two evil team leaders with Weather Ball, Ruby tried to take the Orbs from Maxie and Archie's hands, only to find out that they had started to merge with their holders, making him unable to remove them. Realizing that should the Orbs be absorbed completely, they could never be retrieved, Ruby had Kiki use Covet on them, but failed. The Orbs then completely merged with the two men, causing the patterns of Groudon and Kyogre to appear on their arms, indicating that they were now being controlled by the Legendary Pokémon, instead of the other way around. Maxie and Archie grabbed Ruby and Sapphire, and started to fly away, the Orbs' powers being called by Groudon and Kyogre.
After the two Legendary Pokémon had started to battle at Sootopolis City, Ruby and Sapphire realized that with the Meteorite fragments given to them by Winona, they could stop the Orbs' influence over Maxie and Archie, due to them having the ability to stop the power of nature. Using a wildAbsol's Magic Coat to reflect the meteorite's energy at the two evil team leaders, Ruby and Sapphire were able to turn them back to normal, but also caused a large burst of energy in the process, knocking the two Trainers unconscious. They later woke up at the Mirage Island, where they then spent some time training with Juan, Tate, and Liza, preparing for the final battle. During the training, Ruby found out that the Orbs needed a human to control them, so that their powers could be maximized, and be absorbed into their controllers. This led him to realize that the Orbs were now inside of him and Sapphire, having chosen them as their new controllers. Juan told Ruby and Sapphire that they needed to learn to control the Orbs, because if their minds weren't strong enough, they would wind up getting controlled by them, just like Maxie and Archie. During the training, Magma Admin Courtney showed up and offered her help for Ruby to stop the battle between Kyogre and Groudon, as everything had already gone beyond anything Team Magma or Team Aqua wanted, and there was no point of letting the entire Hoenn getting destroyed. At first, Ruby was reluctant to accept the offer, but eventually agreed in order to protect Sapphire from being possessed by the Blue Orb.
After completing their training, Ruby and Sapphire left the Mirage Island and arrived near Sootopolis City. Having already extracted the Red Orb from his body and having Sapphire extract the Blue Orb from her body, Ruby locked her inside Wallace's aircar to protect her, before leaving with Courtney. They tried to stop the battle between the two Legendary Pokémon, but without success. However, as Norman arrived with Rayquaza, the third super-ancient Pokémon of Hoenn, Ruby was able to combine its power with the power of the Orbs to finally stop the fight and calm down Kyogre and Groudon, sending them to continue their slumber. Archie and Maxie then emerged from the Cave of Origin, stealing the Orbs back in order to restart the fight, but were stopped by Plusle and Minun. With the two men immobilized, Ruby sent out his sixth Pokémon—Celebi—to swipe the Orbs and destroy them, effectively putting the conflict to its end.
Afterwards, the gemstones that were formed from the shattered Orbs were picked up by Giovanni, who revealed that these gemstones were actually the Orbs' true forms: the Ruby and Sapphire. Blaise secretly witnessed this, and decided to keep track on the Orbs with his Scanner.
Bill revealed that the Ruby and Sapphire, which he had been keeping at the Sea Cottage ever since Team Rocket's defeat, had been regenerating over time back into their states as the Orbs, leading him to realize that the Orbs were manifestations of Hoenn's natural energy. The Orbs were later stolen by Archie and Maxie, who headed back to Hoenn with them, with Red and Green in hot pursuit. When Amber and Blaise manipulated Hoopa into summoning Groudon and Kyogre through its rings, the two super-ancient Pokémon started moving towards the Orbs. When the Legendary duo reached Maxie and Archie, the villainous team leaders let them fuse together with the Orbs, causing them both to undergo Primal Reversion.