When Team Rocket entered the Holy Land, they were saved by Dragonite when they fell out a cave. Team Rocket deceived it, claiming they were protecting the Dragon Fang from "thieves", in order for Dragonite to attack the heroes with Hyper Beam. Dragonite then flew off and carried Team Rocket away.
It took them to a vault, containing the prayer flame, where it gave them some food. While it was asleep, Team Rocket snuck into the vault and as they were to steal the prayer flame, the flame burned James' hands. This caused him to drop the flame by accident, which started a fire and angered Dragonite. It attacked Team Rocket, attacking them with Hyper Beam twice. Wobbuffet used Mirror Coat when she attacks them with another Hyper Beam, causing Dragonite to take heavy damage, but it returned and appears more angrier and attacked them with Hyper Beam. Charizard's Flamethrower stopped the attack and gained Dragonite's attention which both Charizard and Dragonite are glaring each other angrily. Clair tried calming Dragonite down, who refused to listen and launched Hyper Beam. Charizard protected Clair, who was still blown the attack, while the group noticed Dragonite was suffering from an Outrage. Pikachu used Thunder, but was canceled by Dragonite's Slam. Dragonite continued attacking, but was hit by Charizard. Charizard launched Flamethrower, making Dragonite fall into the lake. She was not stopped, however, and launched Hyper Beam on Ash, but Clair's Dragonair used Safeguard to protect him, then Dragonair tried to bind Dragonite with Thunder Wave but she manages to break the bind. Ash's Charizard and Clair's Dragonair launched both of their Flamethrower and Hyper Beam at the same time. Dragonite became even more angry and attacks Dragonair by taking it down and negated Charizard's Seismic Toss and threw it on the ground with Slam. While Dragonair summons thunder clouds, Charizard fired a Flamethrower, which Dragonite negated the attack. However, Dragonite got struck by Dragonair's Thunder and Pikachu added the damage with his own Thunder. Dragonite tried to retaliate with Hyper Beam, but was countered by Charizard's Fire Spin. Dragonite suffered too much damage and fell in the lake. Dragonite emerged out and while she was not confused, Dragonite cried at seeing how much the ground was burned while being comforted by all of the wild Pokémon that Brock and Liza tried to save them from the forest fire.
Eventually, Clair caught the Holy Land's Dragonite. Upon arriving to Decolore Islands, Dragonite flew away from Clair, into a field of flowers. Iris' Dragonite appeared and accidentally landed on a flower. This made Clair's Dragonite gets angry and she angrily tackles Iris' Dragonite causing the latter to get mad too as both of them creating a strong argument and its rivalry. Ash's Charizard does its best break the two off but both Clair and Iris' Dragonite angrily pushes him away. Clair, Iris and the others stopped them both, making Cilan believe both Dragonite were just in love with each other and that was the sign of their affection. Later on, the group found an obstacle. Despite their rivalry, Iris' and Clair's Dragonite managed to push away an obstacle. Due to the sound waves emitted from the cave, Clair called her Dragonite back.