In Pokémon Colosseum
Cipher is a criminal syndicate, who has operations in the region of Orre. They basically rule the entire region, and own all of the many coliseums. They are commanded by the mayor of Phenac City, Es Cade, who at first sight seems to be a harmless politician, but has a nasty side hiden behind his clam demeanor. They're sphere of influence stretches through Phenac City, Pyrite Town, and The Under, an underground city controlled by Cipher Admin Venus.
Their Bases of operations are in Pyrite Town, The Shadow Pokémon Lab in The under, and their headquarters, Realgam Tower. Cipher's goal is to use Shadow Pokémon as weapons in battle, and to ultimately dominate all of Orre. The Shadow Pokémon they use are corrupted in the Shadow Pokémon lab in The under, where the head of the lab, Cipher Admin Ein, oversees their production. They are closely affiliated with Team Snagem.