Clair, along with Dragonair, appeared in the opening scene of Pokémon: Johto League Champions.
Dratini was sleeping and was guarded by Clair and her Gyarados. Due to its nature to shed its skin as it moved on the river, Clair followed it. The heroes approached Dratini and were nearly attacked by Gyarados. Clair was told the heroes didn't mean any harm. When Team Rocket attempted to capture it, Clair protected Dratini and had Gyarados blast Team Rocket away by its Hydro Pump after it was strong enough to negate Jessie's Arbok's attack. However, Team Rocket did not stop and disguised themselves as elderly people and captured Dratini in a net with their improvised cane. Clair was seriously determined to save Dratini, who angrily shook Team Rocket's balloon when it dislikes Jessie's pretentious behavior. Dratini attempted to escape from them and fell down. Before it could go back to Clair, Dratini was stopped by Jessie. The heroes and Clair soon arrived and confronted Team Rocket. When Pikachu unleashes its Thunderbolt, Jessie's Wobbuffet countered the attack causing everyone to be nearly hit; Dratini was about to be hit, though Clair managed to save it from a direct hit. Just then, Dratini evolved into Dragonair, which amazed Clair, knowing it was just storing its energy to evolve.
Dragonair demonstrates its abilities by controlling the weather to zap Team Rocket with a blue lightning bolts and eventually blasts them off with a single Twister after Clair's Gyarados knocks James' Weezing to them with its Hyper Beam. Dragonair was alongside Clair and Kaburagi to do the purification ritual before Clair accepted Ash's challenge in the Gym Battle.
Clair and the heroes were alerted Team Rocket stole the Dragon Fang causing their Gym battle with Ash to be interrupted. Thus, Clair sent Dragonair to follow them with Kaburagi, while the heroes rode their Pokémon into a cave. There, Dragonair used Flash to illuminate the cave, as well as to lead them to the Holy Land. Due to a fire, started by James when they attempt to steal the Prayer Flame inside the Dragon Shrine, Dragonair used Rain Dance to douse the flames. Dragonair also battled an enraged Dragonite along with Ash's Charizard and took Dragonite's Outrage attack using its Whirlwind. Dragonite launched Hyper Beam on Ash, but Dragonair protected him by using Safeguard. It binded Dragonite using Thunder Wave but she manages to break the bind and used Hyper Beam, along with Charizard's Flamethrower, to hit it. Regardless, Dragonite blew Dragonair away, who summoned some thunder clouds and manage to struck Dragonite with its Thunder, allowing Ash's Pikachu to use his own Thunder to pin Dragonite down for additional damage. Dragonite attempts to hit them with Hyper Beam, Ash's Charizard counters it with Fire Spin to knock Dragonite off the lake.
Dragonair was the final Pokémon Clair used during her battle with Ash. Dragonair dodged Ash's Pikachu's Quick Attack and Thunderbolt, then defeated him with Hyper Beam. Just as Ash sent Charizard, the Gym's roof opened, as the battle would be held in the sky as well. Charizard launched Flamethrower, though Dragonair went underwater to escape Charizard's attack. Dragonair retaliated with Hyper Beam, but missed and went in the water to avoid Flamethrower attack. It went out to use Dragon Rage and quickly retreat back in the pool to escape Charizard's Flamethrower. Dragonair fired a Hyper Beam, which collided with Charizard's Fire Spin. Just then, Charizard continued using Fire Spin and doused the water, which made Dragonair unable to hide in the pool due to the water being evaporated. Charizard attempted to fire a Flamethrower, which was negated by Dragonair's Safeguard and Charizard got slammed by its Iron Tail attack. Dragonair attempted to repeat the attack, but Charizard blocked the attack. Just as Charizard was to use Seismic Toss, by using Dragon Rage, Dragonair escaped the attack, causing Charizard to fall down. Dragonair fired another Hyper Beam and missed. Charizard also fired a Flamethrower, which Dragonair evaded and used Iron Tail, but missed. Just as Dragonair used Dragon Rage to escape Charizard's Seismic Toss, the latter used another Fire Spin on the Dragon Rage, causing it to heat up and then slammed Dragonair into the ground with a flaming Seismic Toss, defeating it.
Dragonair was mounted by Clair while she assisted Ash in searching for his eight badges, which were stolen by Team Rocket. Eventually, it was found by a wild Wynaut after both Ash's Bayleef and Totodile found the badge case. It managed to save Ash from falling before Team Rocket was blasted off, as well as to collect the badges.
While recalling the adventures with Charizard, Ash remembered Dragonair, who was using Iron Tail against Ash's Charizard before getting defeated by its Seismic Toss and Fire Spin attack during his Gym battle rematch with Clair.
As Ash, Cilan and Iris encountered Clair, Ash remembered battling alongside Clair. He used Charizard and Pikachu, while she her Dragonair, to defeat the enraged Dragonite, whom Clair eventually caught.