Organizations

Organizations are usually led by the main antangonist other than your rival and going after a Legendary Pokémon.

List of Organizations and their Leaders
Team Rocket-Leader:Giovanni, their goal is world domination. they operate on the continent composed of Kanto and Johto. The legendary Pokémon they created is Mewtwo.

Team Aqua- Leader:Archie, their goal is to cover the earth with water to create more life. They operate in Hoenn. The legendary Pokémon they are after is Kyogre.

Team Magma- Leader:Maxie, their goal is to expand the continents to create more land for life to dwell on. They operate in Hoenn. The legendary Pokémon they are after is Groudon.

Team Galactic- Leader:Cyrus, the goal of the leaders is to re-create the universe in Cyrus's image. They operate in Sinnoh. The legendary Pokémon they are after are Mesprit, Uxie, and Azelf, Palkia, Dialga, and Giratina.

Cipher- Leader:Evice/Greevil: Cipher steals Pokémon and unnaturally shuts their hearts. They operate in Orre. If you consider Tyranitar a semi-legendary, it was their "ultimate Pokémon" in Pokémon Colleseum. In XD Gale of Darkness, they had a "Shadow Lugia" that supposedly couldn't be purified.

Team Snagem- Leader:Gonzap, Snagem wants to steal every Pokémon in the world. They operate in Orre. They have no legendary Pokémon in particular.