Rayquaza

Rayquaza is a dual-type Dragon/Flying legendary Pokémon that resides above the ozone layer, which made his existence debatable until it was recently discovered, and serves as a villain in several of his appearances. His ability, Air Lock, prevents the weather from being altered.

Destiny Deoxys
Rayquaza appears in Destiny Deoxys as the main antagonist. This Pokémon, like most other featured legendary Pokémon, proved to be extremely powerful. It fights against Deoxys because it is seen as invading its territory. After a destructive battle over a glacier witnessed by Professor Lund, Yuko, and Lund's son Tory, and although it takes a few Psycho Boosts and is critically hit and falls into the freezing ocean, Rayquaza comes back and defeats Deoxys with a Hyper Beam attack. Four years later, Deoxys manages to regenerate, and it goes to find its friend, another Deoxys. Rayquaza senses its presence and goes to LaRousse City to battle Deoxys again. After LaRousse City has been evacuated, Rayquaza manages to break through Deoxys's city-wide barrier after many failed attempts. Then, Rayquaza and Deoxys have a second spectacular battle that destroys some of the city. After Deoxys finds its friend and helps fight off the malfunctioning security bots, Rayquaza realizes that Deoxys is not hostile and stops attacking. It (or possibly another of its species) also has a cameo in the opening to the ninth Pokémon movie and is captured by Team Rocket. Its current status is unknown, possibly flying around in the atmosphere (assuming it managed to escape from Team Rocket).

Super Smash Bros. Brawl
Rayquaza appears in the Subspace Emissary mode as a boss. After Diddy Kong lands on a mysterious island, Rayquaza lunges out of the water and snatches him, furious from being disrupted. A ship suddenly crash-lands and smashes onto the beach, and out jumps Fox, who deflects Rayquaza's Dragon Pulse back at it. Rayquaza collapses into the water, but not for long until it launches back out, engaging in battle between Fox and Diddy. Rayquaza fights with strong electrical attacks, digging underground, causing explosions that come out of nowhere, and ramming into it's opponents. Eventually Rayquaza was defeated by Fox and Diddy Kong. Later, it is fought in the Great Maze level again and can be fought in the Boss Battles after the storyline is beaten.

It's been hinted that Rayquaza is in league with the Subspace Army. It's also unclear why Rayquaza was in the lake, when Rayquaza is known as the Sky High Pokémon, and it's said to live in the high areas like the ozone layer or even space.

Trophy Information
''A Sky High Pokémon. It normally resides high up in the ozone layer where it flies endlessly, so it is rarely seen. However, when Groudon and Kyogre began to fight, it appeared to calm them down. It has the ability Air Lock, which blocks all weather-condition effects. It has exceedingly strong abilities, and its attack power is especially remarkable.''

Pokémon Mystery Dungeon Series
In Pokémon Mystery Dungeon Red Rescue Team & Blue Rescue Team he portrays as the final boss. The final boss takes place at Sky Tower. He attacks you and your partner because you disturbed his sleep. After you defeat Rayquaza you convince him that he's the only one to destroy a meteor that can and will destroy the world. He then unleashed a super powerful Hyper Beam and destroyed the meteor. You can also fight him again and on rare occasion he'll ask you to join your team. you can even play as Rayquaza.

In the sequels Explorers of Time, Darkness, and Sky he's the guardian of a very rare item called Sky Melodica, which gives you the ability to befriend flying-type Pokémon a bit more easily. And just like the other Mystery Dungeon games Rayquaza may ask you if he can join your team and play as him.

Pokémon Conquest
In the video game Pokémon Conquest, a man name Nobunaga processes a shiny Rayquaza for one of his Pokémon.