Rhydon first appeared as a wild Pokémon in Rock, Paper...Scizor, rampaging near the Viridian Gym along with an Alakazam, an Arcanine, and an Exeggutor, due to the Pokémon League that was being played in a radio. Seeing that the Pokémon needed to be stopped, Blue used his Scizor to defeat the rampaging Pokémon, which he then caught, impressing the Pokémon Association so much, that they decided to appoint him as the new Gym Leader of the Viridian Gym.
During the Gym Leader exhibition match, where Blue faced his former mentor Chuck, he decided to restrict his use of Pokémon to Rhydon only. At first, Rhydon faced Chuck's Machamp. Although Rhydon managed to hit Machamp with Horn Attack, it proved to be a part of Chuck's strategy, as he then hit Rhydon with Vital Throw, which has a 100% hit rate in exchange for a decreased priority. After this Chuck switched to Hitmonlee, which first avoided Rhydon's attacks with Mind Reader. Although Rhydon managed to eventually strike Hitmonlee, the hit proven to be taken on purpose again, as the Kicking Pokémon then attacked the Drill Pokémon with Reversal. Chuck then once again switched his Pokémon, now sending out Hitmontop. Trying to seek an optimal moment to hit the opponent, Blue had Rhydon destabilize the ground with Earthquake. However, Hitmontop just took an advantage of the situation, escaping into the air before striking Rhydon with its head spike. When Hitmontop prepared for another strike, Blue recalled the lessons he had learned from Chuck, feeling the movements and connecting those feelings to his Pokémon. Using this as his advantage, Blue had Rhydon cancel out Hitmontop's spin and attack it with Horn Drill, defeating the Handstand Pokémon and winning the battle for Blue. After the battle, Blue revealed Chuck that he had chosen to use only Rhydon because after being appointed the Gym Leader of Viridian, he had discovered a secret guide hidden in there, labeled Secrets of the Land and written by the previous Gym Leader of Viridian, who had been a Ground-type specialist. Seeing that he was the new Leader of the Gym, Blue explained that he felt that he should decode the guide and master the techniques it described.
Later during the chapter, Blue used Rhydon to dig a tunnel to the Ilex Forest.
During the FireRed & LeafGreen arc, Blue used Rhydon in his Battle Path match against Red. Later Rhydon was used to defeat Orm, freeing Blue and his Pokémon from the grasps of the Shuckle that Orm's Shuckle had been commanding. Close to the end of the chapter, Rhydon was one of the Pokémon that the Pokédex Holders used to slow down the Team Rocket airship during its crash-landing.
During the HeartGold & SoulSilver arc, it was revealed, that in order to help Silver fill out his incomplete team, Blue had traded Rhydon over to him, allowing the Drill Pokémon to evolve into Rhyperior, thanks to the Protector it had been holding.
