With Misty
Gyara debuted in Gyarados Splashes In!, attacking his original Trainer, Misty. Red shows up and decides to help by sending out Saur. Saur, alongside Misty's Staryu, manage to weaken him enough to be recaptured by Red, who returns him to her. Later on it is revealed that the drastic change in his attitude was the result of a Team Rocket experiment, where Koga shamelessly remarks, "Hmm? How should we know of every Pokémon we experiment on?", earning Misty's rage.
In What a Dragonite, Gyarados is sent out by Misty to fight against a wild Dragonite that was attacking Red underwater. Gyarados manages to distract Dragonite long enough for Misty to get Red to the surface. Once the two dragons emerge the Dragonite shoots off a Hyper Beam, and Red has Gyarados counter back with his own. As the smoke clears from the clashing attacks, Dragonite falls back into the waters, defeated.
With Red
In You Know...Articuno!, Misty offers to give Red Gyarados in exchange for his Krabby since Gyarados knew how to use Surf, which Red accepts. Although Red was happy to have obtained him, his earlier ferocity got him isolated by Red's other Pokémon. When they ran into Team Rocket again, Gyara was forced to relive some painful memories of his experimentation. Red had his other Pokémon help him through that traumatic experience and after that he was broken into the group, resulting in Red's Pokémon trusting him more.
In Can You Diglett?, Gyara is shown in a flashback fighting against Bruno's Onix. Gyara attacks with multiple Hydro Pumps, but Bruno's Onix dodges them all by twisting its snake-like body. Onix then gets close and uses Bind, immobilizing Gyara. Red sees that Gyara can still use his head and has him attack with Bite. Onix then Digs underground in order to avoid the next attack. After seeing this Red recalls him.
In Rock, Paper...Scizor, Gyara is temporarily traded to Blue for his Charizard. In Entranced by Entei, he is used to battle against a wild Entei. Alongside Silver's Gyarados, the two fire powerful Dragon attacks, though Entei shrugs them off and flees.
By the start of the FireRed & LeafGreen chapter Gyara has been returned to Red. In Red and Blue Make Purple Opponents, Gyara is used alongside Snor in a double battle against Blue and his Golduck and Porygon2. Gyara starts the battle off with his Ability Intimidate, and Blue responds by having Golduck use Iron Tail and Porygon2 use Tri Attack on Red's Pokémon. Red then has Gyara counter attack with Body Slam on Porygon2, while Snor attacks Golduck with Strength. Gyara next uses Hyper Beam on Golduck, and Golduck uses Dig to hide and avoid further damage. Red counters by having Snor use Earthquake, dealing damage to Porygon2, twice the damage to Golduck due to him being underground, which causes him to faint, and Gyara being unaffected due to him being part Flying-type. As Red celebrates he notices that Gyara had been paralyzed by the effects of Tri Attack. Gyara is then attacked by Scizor's Steel Wing and defeated.