In Subspace Emissary, it suddenly emerges from a lake after hearing Diddy Kong, who had been looking at the nearly destroyed Arwing nearby. It attacks the Arwing with Dragon Pulse and snatches Diddy in its claws. Diddy screams for help, whereas Fox McCloud, who manages to escape the damaged Arwing, leaps from the Arwing and breaks Diddy free of Rayquaza's grasp using Fox Illusion. Rayquaza, furious, ends up using Dragon Pulse on Fox, who deflects it with Reflector, flinging it back at Rayquaza, who falls back into the lake.
Fox and Diddy engage in a fight with Rayquaza, resulting in the second main boss fight of the Subspace Emissary. Some of its attacks involve burrowing into the ground and then bursting upwards. It also flies with great speed horizontally over the stage and sometimes drops a Thunder attack. The player can beat it by attacking it around the head. When Rayquaza uses Dragon Pulse, the player can use Fox's Reflector to counter it.
Although Rayquaza does not appear to have any connections with the Subspace Army, it is fought again in The Great Maze. Rayquaza is also the only non-playable Pokémon and non-Poké Ball Pokémon to get its own Sticker.
Rayquaza also appears in Super Smash Bros. for Wii U and Super Smash Bros. Ultimate as a stage hazard for the Kalos Pokémon League stage. It sometimes appears at the Dragon-type chamber, where it damages anyone that it comes into contact with. In Super Smash Bros. Ultimate, Rayquaza also appears as a spirit.
Super Smash Bros. Brawl
Super Smash Bros. for Wii U
Names in other languages