Rayquaza is a legendary Pokémon from the third generation of games in the Pokémon series. It is based off a Chinese dragon, and the Ziz, a huge mythical bird of Jewish myth, often coupled with the Leviathan and Behemoth (or in the case of Pokémon, Kyogre and Groudon).
According to the Pokédex, Rayquaza has lived in the upper ozone layer of the atmosphere for hundreds of millions of years, surviving on water molecules and stray particles as it circles Earth at incredible speeds. When seen from the ground, it appears to be a shooting star or comet. "Rayquaza" comes from the words ray and quasar, adding to the idea that it comes from beyond Earth.
Rayquaza, Kyogre and Groudon make up what fans call the Trinity, the legendaries of R/S/E. Rayquaza represents the sky in this trinity, with Kyogre representing the sea, and Groudon representing land. It is said that if Groudon and Kyogre ever get into a fight, Rayquaza descends from the sky to ensure balance is restored -- perhaps referencing the battle between Team Aqua and Team Magma in R/S/E.
Rayquaza also represents Pokémon Emerald, and is featured on its boxart.