Two years prior to the Ruby & Sapphire arc, Minun, along with Ruby's Plusle, was owned by a passenger on the Abandoned Ship. After their owner's death, Minun and Plusle became wild Pokémon and made the Abandoned Ship their home.
When Ruby arrived on the Abandoned Ship in Adding It Up with Plusle & Minun I, Minun and Plusle began attacking him as a prank. When Ruby managed to discover the two pranksters' identities, Minun and Plusle used their cuteness to lure Ruby into a false sense of security before continuing with their antics. After seeing through their pattern, Ruby realized that Minun and Plusle were attempting to keep him away from a room, which he assumed to be holding a rare type of Berry. When Ruby attempted to open the room's door, he was attacked by Tabitha, a member of Team Magma, who aimed to take the Scanner held inside. Minun and Plusle attempted to stop Tabitha, but were easily defeated. Ruby and Sapphire team up with Minun and Plusle and use them to battle against Tabitha and Courtney. Through teamwork, Ruby and Sapphire manage to win the battle and escape, but lose the Scanner to Tabitha and Courtney. Afterward, Minun and Plusle say their goodbyes as Ruby and Sapphire head off to continue with their journeys.
When Kyogre is awakened, it surfaces around Route 108, where it proceeds to blast the Abandoned Ship, destroying it. Minun and Plusle are caught up in this attack, but are able to escape the destruction of their home.
Minun and Plusle eventually arrive on Mirage Island, where they encounter Ruby and Sapphire in With a Spoink in Your Step II. They decide to assist Ruby and Sapphire by joining their teams and training with them to master Double Battles. Once their training had finished, Ruby and Sapphire leave Mirage Island and prepare to head to Sootopolis City in order to stop the clash between Kyogre and Groudon. Due to worrying about Sapphire's safety, Ruby shoves Sapphire, Minun, and Plusle inside Wallace's aircar and locks them in. He then goes off to stop Kyogre and Groudon, leaving the three behind.
Although Ruby succeeds in stopping the fight, he is attacked by Archie and Maxie shortly afterward. Minun and Plusle use their electrical attacks to try and open the barrier created during Kyogre and Groudon's battle, but are unable to make a hole large enough. They are assisted by the arrival of the Trick Master, who uses the New Mauville generator to boost Minun and Plusle's powers, giving it the strength needed to make a hole large enough to travel through.
After Ruby and Sapphire defeat Archie and Maxie, the two Leaders steal Wallace's aircar and use it to make their escape. By using Minun and Plusle, Ruby and Sapphire trap Archie and Maxie in a giant electrical sphere, finally defeating them.
In the Omega Ruby & Alpha Sapphire arc, it is revealed that Minun and Plusle had been released back into the wild. During a trip to the Sea Mauville in Omega Alpha Adventure 5, Sapphire meets with Minun and Plusle again. During the battle against Zinnia, Minun and Plusle assist in helping protect the dimensional shifter.
