Gyarados first appeared when it was used to protect Clair's Dragonair while it was a Dratini. Thinking that Dratini was under threat, Gyarados attacked Ash, Misty and Brock with Hydro Pump, but stopped when Clair realised that they meant no harm. Once Team Rocket came to capture Dratini, Gyarados blasted them away with Hydro Pump. During the second battle, Gyarados repeated Hydro Pump, but was reflected by Wobbuffet's Mirror Coat. Just as Clair's Dratini evolved into a Dragonair, Clair's Gyarados used Hyper Beam to protect it from Weezing's Sludge, allowing Dragonair to blast them away with Twister.
Gyarados was a powerful fighter and was used in Clair's second Gym battle with Ash. Gyarados countered Ash's Snorlax's Hyper Beam with Hydro Pump and paralyzed it with Dragon Breath. With Hyper Beam, Gyarados defeated Snorlax. Ash sent out Pikachu, whose Quick Attack dodged Gyarados' Hyper Beam and hit the giant Pokémon. Gyarados attempted to bite and used Dragon Breath against Pikachu's Thunderbolt. Gyarados managed to wound Pikachu with Hydro Pump and wrap it with its tail. Pikachu was freed by using Thunderbolt, while Gyarados tried to use Bite. Pikachu avoided the attack with Agility, then walked on Hydro Pump attack and defeated Gyarados with Thunderbolt.
When Team Rocket stole Ash's badges, the latter was searching for the lost badges. He also remembered his battles with the Johto Gym Leaders, including Clair and her Gyarados, as Ash and his Pokémon won those badges with hard effort.