Deciding to cooperate with the Hoenn Champion, Alain and company traveled to their destination, a small temple with two pillars in the center. When Alain and Steven held their Key Stones to the monument, a staircase of light appeared to lead them further within the ancient ruin. There, they discovered a similar mechanism that summoned a glowing megalith from underneath the ruin. After Lysandre and his research team began analyzing the giant stone, a Rayquaza appeared from the sky, Mega Evolved into Mega Rayquaza, and started wreaking havoc on the surrounding area. Alain, Steven, and their Mega Pokémon partners tried to fend off the Legendary Pokémon, but were overwhelmed. As Rayquaza continued to destroy the megalith, its Draco Meteors landed near Mairin, sending her and Chespie flying. Alain dove to save her, but in the process, the two are buried in debris. Mairin is safe, but Alain injures his shoulder. Despite Mairin and Lysandre's concern, Alain insists he's fine, and proceeds to Rustboro City on Lysandre's orders as he believes the megalith can be recovered, secretly he told Alain to keep a watch on Steven Stone, as he possessed great knowledge on Mega Evolution.
In Mega Evolution Special III, after landing at the Devon Corporation headquarters via helicopter with Mairin, he receives confirmation from Steven and Lysandre that Primal Groudon and Primal Kyogre are set to battle each other near Rustboro City to claim the megalith's energy, putting the entire world at risk. Alain and Steven volunteer to fly to the point where the super-ancient Pokémon will meet to analyze the situation. Concerned, Mairin asks Alain about his shoulder, but Alain insists he's fine. Mairin says it's too dangerous, and begs Alain to stay, but he refuses, saying he has to keep his promise to Lysandre to become the strongest. Mairin continues to press him, causing Alain to lash out at her, saying she knows nothing about his goals. After calming down, Alain walks away from Mairin, telling her to go back to Kalos.