In the games, the player encounters the Red Gyarados while exploring the Lake of Rage. Once it is either caught, or defeated, the player will be able to enter the Team Rocket HQ hidden in the shop in Mahogany Town.
At the beginning of Pokémon Diamond, Pearl, and Platinum, Barry and the player hear about a Red Gyarados sighting on the news, and travel to Lake Verity hoping to find a similarly rare Pokémon.
The Red Gyarados made its anime debut in Talkin' 'Bout an Evolution! where Team Rocket were conducting an experiment to draw out the Red Gyarados. In the end, Lance ended up catching it and promised to take care of it. It later appeared alongside Lance in Gaining Groudon and The Scuffle of Legends during the fight between Groudon and Kyogre.