Lysandre sent Gyarados to intimidate Tierno, Shauna and Trevor, wanting to see pictures Trevor took in Vaniville Town. Fortunately for the kids, Diantha arrived with her Gardevoir, claiming Lysandre has frightened the children too much. Later on, Lysandre was called for an important meeting and went off with Gyarados, claiming it was "one of the chosen ones".
Gyarados was with Lysandre, who prepared himself to activate the Ultimate Weapon. After X infiltrated the Team Flare headquarters, he faced Lysandre. Lysandre showed him Korrina's Key Stone on the ring he wore and touched it, starting to Mega Evolve Gyarados. To continue his battle against Lysandre, X called his Quilladin and Charmeleon back and sent Manectric, Gengar and Kangaskhan. Mega Gyarados bit X's Manectric, who used Wild Charge and electrocuted Mega Gyarados. X noticed Mega Gyarados took less damage than a normal Gyarados would, as well as its Bite attack caused more damage, suspecting Mega Gyarados' type changed to water/dark. Lysandre commended X for the observation and continued the battle. X fooled Lysandre, who, in distaction, did not notice X Mega Evolved Kanga, who bashed Mega Gyarados' head.
After Shauna, Tierno and Trevor arrived to Lysandre's chamber, they noticed Lysandre, Mega Gyarados, Mienfoo and Pyroar, who managed to defeat X and his Pokémon. Xerosic tried to stop the children from leaving the chamber; however, Lysandre, standing on his Gyarados, claimed there was no need, since he claimed to have succeeded in their operation.
Lysandre was training with Mega Gyarados at the Pokémon Village, where he had it use Waterfall. X dreamed of Lysandre and his Mega Gyarados, who defeated him and his team. X soon woke up, realizing he was afraid of them.
Lysandre watched on Gyarados how Blue and X were facing Mewtwo. Much to his surprise, Mewtwo fired Psystrike on him and Gyarados before Mega Evolving. Lysandre Mega Evolved his Gyarados, who attacked Mega Mewtwo, after Zygarde attacked Lysandre's enemies. Seeing X wanted to defeat Essentia, Lysandre's Mega Gyarados attacked him before getting hit by Y's Solsol. To stop Lysandre, Y had her Mega Absol bite his arm. Pyroar used Noble Roar to stop Solsol, who succeeded in taking Lysandre's Key Stone from his finger. This caused Gyarados to revert to its original form. With five Mega Evolved Pokémon, X charged in to defeat Lysandre and his Pokémon. In the end, both of them were defeated by Blue and Mega Mewtwo.
- ^ X&Y004: They Have a Flare for a Li'l Kanga-Napping
- ^ X&Y011: Chespin Sows the Seeds of Change
- ^ X&Y029: Quilladin Stands
- ^ X&Y030: Gyarados Changes
- ^ X&Y031: Pyroar Breathes
- ^ X&Y032: Flabébé Blooms
- ^ X&Y033: Rhyhorn Charges
- ^ X&Y035: Scizor Defends
- ^ X&Y039: Malamar Traps
- ^ X&Y042: Yveltal Steals
- ^ X&Y043: Mewtwo Angered
- ^ X&Y044: Zygarde Agitated
- ^ X&Y045: Xerneas Gives