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.
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 quickly gets him isolated from 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 Holy Moltres, Red faced against the Legendary bird Moltres, which was under the control of Team Rocket. Despite the type advantage Gyara was unable to defeat the Flame Pokémon, and Blaine realized that to stand a chance against the Flying-type Pokémon, they needed a Flying-type of their own. When seeing Red's Old Amber, Blaine sent him to the Island's laboratory, with Gyara staying behind to stall Moltres. Blaine and Gyara were soon overwhelmed, but were saved when Red arrived with Aero.
As revealed in Quilava Quandary, Gyara was a part of the team Red used during the Pokémon League.
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 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. Soon after Gyara, alongside Saur and Snor, were called out to battle Lorelei, Bruno, and Agatha. With the power of the Badge Energy Amplifier, the Elite Four's Pokémon do a combination attack of Ice, Fighting, and Ghost powers, knocking the three out.
In Rock, Paper...Scizor, Gyara is temporarily traded to Blue for his Charizard. In Entranced by Entei, he battled against a wild Entei. Alongside Silver's Gyarados, the two fire powerful Dragon attacks, though Entei shrugs them off and flees.
By PSs1, he has been returned to Red.
Gyara appeared in a fantasy in Rayquaza Redemption II, when Sapphire explained to Ruby that the accomplishments of Red and his team inspired her to train to battle.
In Red and Blue Make Purple Opponents, Gyara battled 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.
In Don't Doubt Deoxys, Gyara is used to battle against Organism No. 2. Gyara was later nearly killed along with Red's other Pokémon while defending his Trainer from Organism No. 2's Psycho Boost.
In Distant Relation Deoxys and Storming the Forretress, Gyara was seen joining Red's other Pokémon, Blue's Charizard, and Chuchu to take down the ten Forretress that Carr had placed inside the Team Rocket airship.
Gyara appeared in a flashback in All About Arceus IX, when Hirō explains that he based Proteam Omega off of Red's team after watching him train on Mt. Silver.