Prior to Raise the Red Gyarados, Gyarados was the leader of a group of Magikarp at the Lake of Rage. When Team Rocket used the Goldenrod CityRadio Tower to disturb Pokémon with their evolution-inducing waves, the Magikarp started to suddenly evolve into Gyarados and began to act crazy. When Gold and Silver arrived and saw what was happening they began attacking the Gyarados while searching for the signal that was causing it. Gyarados soon pops up from out of the water and Gold's and Silver's Pokégears have an even stronger connection, meaning that he was the source of the waves. The two decide to capture him to stop the waves and have Polibo and Murkrow weaken him, allowing Silver to catch him.
In Delibird Delivery - 2, Gyarados fought against the Masked Man. Silver had Gyarados bring all the Gyarados that were forcibly evolved upon the Masked Man and has them launch a powerful Hyper Beam. The attack is later seen to have failed as the entire lake is frozen and Silver is unconscious.
In Do-Si-Do with Dodrio, it is revealed that Gyarados was frozen at the bottom of the Lake of Rage. After Lt. Surge finds him he wakes up and immediately rushes over to where he thinks Silver is and attempts to break him out as well, but fails due to his exhausted state. Lt. Surge breaks the ice open for him and discovers some of Gold and Silver's things. Realizing they have a connection to the Masked Man he decides to take Gyarados with him and heads off to Morty to search for the two. In Sandslash Surprise, Gyarados is returned to Silver.
In Surprised by Sneasel, Gyarados battled Sird and her Banette. Gyarados attacks with a Fire Blast but it is dodged and Banette counters with Shadow Ball. Gyarados then tries to heal his injuries with Rest, but Banette eats the move with Snatch, allowing herself to be healed instead. Banette attacks Gyarados with a Double-Edge and Silver retaliates by having Gyarados attack with Fire Blast again. Yellow and Orm's battle soon starts and Orm's Jumpluff releases several spores which have multiple different effects. One of them hits Gyarados and puts him to sleep, taking him out of the fight.
In Storming the Forretress, after Giovanni was defeated and Carr sent the flying airship containing him, Silver, his loyal subordinates, and enemies crashing, Gyarados teamed up with the other Water-type Pokémon to try to keep the airship in place. However, ultimately, it was Mew who saved it.
In Weavile Wobbles But It Won't Fall Down, Silver used Gyarados while facing Petrel for the first time in the Safari Zone. Gyarados first saved Silver from a falling bridge and after that was used as intimidation in order to get Petrel's Plates. He was later seen training alongside Silver's other Water types.
When Silver first met Gyarados he displayed typical characteristics of his species. He was shown as angry and enraged, attacking every nearby person and Pokémon and not calming down for a second, although this was due to his rage at Team Rocket's evolution waves. Gyarados is an extremely powerful Pokémon and was once the leader of a group of Gyarados. Gyarados also cares greatly for his Trainer, shown when he wore himself down to exhaustion trying to save him from his ice imprisonment despite only being caught recently.
Gyarados is the only one of Silver's Water-type Pokémon that did not evolve under his ownership, as it was caught already in his final stage, unlike Kingdra and Feraligatr, who were received in their initial stage.