Rayquaza first appeared when Alain, Mairin, Steven Stone and Lysandre were searching for the megalith in some ruins. Rayquaza evolved into its Mega form and wanted to have the megalith. Alain used his Mega Charizard X and Steven, his Mega Metagross, to attack Rayquaza and to defend the megalith. Rayquaza easily defeated Charizard with Dragon Pulse and Dragon Ascent, destroying the ruins with many rocks flying around and creating some smoke. After the smoke cleared up, Rayquaza and the megalith were both gone and Rayquaza was seen flying around in space in its normal form.
Rayquaza later appeared again in its Mega form when Groudon and Kyogre were battling for a megalith. Rayquaza used several attacks to stop them while Steven's Metagross was battling them as well. It later finished both Groudon and Kyogre off by using Dragon Ascent, returning them both into their normal form instead of the Primal form. After both of them were gone, Rayquaza wanted to grab the megalith but a submarine emerged and grabbed the megalith instead.