Rhyperior first appeared as a wild Rhydon in Rock, Paper...Scizor. He, along with an Alakazam, Arcanine, and Exeggutor, rampaged near Viridian City after being attracted by the sound of the Pokémon March being played by a Pokémon Association van's radio. Blue used his Scizor to defeat the rampaging Pokémon, which he then caught. The Pokémon Association were impressed so much that they decided to appoint him as the new Gym Leader of the Viridian Gym.
In Entranced by Entei, during the Gym Leader exhibition match at the Indigo Plateau, Blue faced his former mentor, Chuck. During this battle, Blue decided to only use Rhydon. Rhydon first went up against Chuck's Machamp, which let Rhydon hit first so that it could use Vital Throw, which always makes the user go last. Next, Chuck switched Machamp with his Hitmonlee, which used Mind Reader to dodge Rhydon's attacks. Rhydon managed to grab Hitmonlee's stretchy legs and attacked with Stomp, only to be countered with Reversal. Chuck then switched Hitmonlee for Hitmontop, which greatly damaged Rhydon with his ability to attack multiple times while spinning. Eventually, Chuck had Hitmontop attack from the air by using his horn as a drill. Rhydon countered with his own Horn Drill and caused Hitmontop to slow down by reversing the rotation of his drill, leading to Hitmontop's defeat and Blue's victory. After the battle, Blue revealed he trained Rhydon to a high level with a book titled Secrets of the Earth, which was written by the previous Viridian Gym Leader, who had been a Ground-type specialist.
In The Last Battle IX, Blue had Rhydon dig a tunnel to Ilex Forest so that he and Red could help their allies confront the Masked Man. During the trip Rhydon had a quick battle against Koga and his Tentacruel, but it was stopped when Koga revealed he wasn't there to fight.
In Double Dealing with Deoxys, Rhydon participated in Blue's battle against Red to determine which one would learn one of the ultimate moves from Ultima. With his Lightning Rod Ability, Rhydon redirected the Electric attacks fired by Pika to prevent them from hitting Machamp.
In Don't Doubt Deoxys, Rhydon battled against Orm and his Shuckle on Six Island. With his drills, Rhydon broke the horde of Shuckle Orm was using to keep Blue pinned down.
Near the end of the fifth chapter, Rhydon helped to slow the descent of Team Rocket's airship to prevent its crash-landing into Vermilion City. However, ultimately, it was Mew who saved it. Afterwards, Blue gives Silver the book Secrets of the Earth, telling him that the book suggests that Rhydon can evolve further and that the evolution involves trading. Since trading is Silver's specialty, Blue tasks Silver with discovering the process.
In The Final Battle VII, Rhydon appeared alongside the rest of Blue's team when he was checking to make sure they all survived the petrification caused by Mewtwo and Darkrai.
Rhyperior while under Silver's ownership
In Raising the Stakes with Rhyperior, it was revealed that Blue and Silver traded Pokémon. With the Protector he received from Silver, Rhydon evolved into a Rhyperior. Afterward, Blue then decided to give Rhyperior to Silver so that he may fill the missing slot in his party. Rhyperior was first seen with Silver battling Ariana on Route 38. With an Earth Plate-boosted Earth Power, he distracted Ariana long enough for Silver to escape and head to Ecruteak City to meet with Morty. When Silver arrived at the Ecruteak Gym, he was stopped by Falkner, Bugsy, and Chuck, who were protecting the Gym from suspicious people under Morty's request. Having no time to explain the situation, Silver battled the three Gym Leaders in order to force his way into the Gym. Chuck used his Hitmontop to battle against Rhyperior, but the two Pokémon stopped when their drills collided, both realizing that they had fought each other in the past. After Silver explained who Rhyperior originally belonged to, Chuck decided to trust Silver and allowed him into the Gym.
In All About Arceus VIII, Rhyperior battled Giratina to protect Silver's father. Silver then revealed that he decoded Giovanni's book, which allowed him to teach Rhyperior Rock Wrecker.
In Pinsir Glares, it was revealed that Blue took Rhyperior back from Silver in order to help him find Zygarde. Rhyperior was first seen helping Diantha emerge from underground, where she was put in order to escape the blast of the ultimate weapon. He, along with Charizard, later led X's group to Anistar City, after which they left and returned to Blue.
In Yveltal Steals, Rhyperior tried to help suppress Mewtwo's rage at the Pokémon Village alongside Charizard, Marisso, and Salamè. Despite their numbers, Mewtwo kept the advantage, easily knocking them away with Psywave.