From Bulbapedia, the community-driven Pokémon encyclopedia.
Groudon and Kyogre battle as Rayquaza arrives.
The weather trio, also less commonly referred to as the elemental trio, is the legendary trio made up of Groudon, Kyogre, and Rayquaza. They are referred to in the games as the super-ancient Pokémon (Japanese: 超古代ポケモン super-ancient Pokémon), although the Japanese anime has applied this term to Fossil Pokémon as well.
The weather trio could be references to the Biblical mythologies, Leviathan, a sea monster; Behemoth, a land beast; and Ziz, a giant bird, respectively. Also, their role as the guardian, as well as their respective typing, are related to the elemental spheres; Kyogre being the hydrosphere, Groudon being the lithosphere, and Rayquaza being the atmosphere. These three members all appear to have similar physiology; identical signs on their body, as well as their yellow eyes.
Although several non-legendary Pokémon, such as Tyranitar and Abomasnow, have Abilities that can alter the weather conditions, and Pokémon with the Ability Cloud Nine are capable of stopping weather effects altogether, Groudon, Kyogre, and Rayquaza's Abilities were the first sight of these weather-changing ones in the games. This makes them the first legendary trio not to share one universal Ability.
Unlike Pokémon with moves like Sunny Day and Rain Dance, where the weather changes to another for only five turns, the Abilities of the legendary trio cause their weather effect for the remainder of the battle, or until the weather is changed again in some way. Rayquaza's, however, only lasts as long as it remains active, and with its Air Lock, which removes the battle effects of any weather on the field, leaving it to just be a pretty-looking environmental effect.
They do not appear to have a Trio master, though Rayquaza seems to serve as the leader of the three internally. It was shown quelling a violent confrontation between the other two Pokémon during the events of Pokémon Emerald.
This, the Tao trio and the Kami trio are the only legendary trios whose members do not all have the same base stat total; Groudon and Kyogre share a total of 670, while Rayquaza's is 680. This fits with its role as a mediator between Groudon and Kyogre.
Base stat comparison
In the games
Pokémon Ruby and Sapphire
In the Generation III Hoenn games, both Kyogre and Groudon appear in the Cave of Origin, and after the defeat of the Elite Four, the player can encounter Rayquaza at rest on the topmost floor of the Sky Pillar.
In the enhanced version of Ruby and Sapphire, Kyogre and Groudon both appear in alternating caves after beating the Elite Four: Marine Cave (on Route 105, Route 125, Route 127, or Route 129) for Kyogre and Terra Cave (on Route 114, Route 115, Route 116, or Route 118) for Groudon. Rayquaza appears atop the Sky Pillar after calming Kyogre and Groudon in Sootopolis City, and is obtainable before the defeat of the Elite Four.
Pokémon HeartGold and SoulSilver
All members of the weather trio can be obtained in the Embedded Tower after Red is defeated and player has the National Pokédex, Kanto starter Pokémon, and respective Orbs. Kyogre is obtainable in HeartGold, and Groudon is obtainable in SoulSilver. Once both a Kyogre from HeartGold and a Groudon from SoulSilver are in one game, the player gets an opportunity to catch Rayquaza.
Embedded Tower Kyogre.png
Embedded Tower Groudon.png
Embedded Tower Rayquaza.png