Cipher (called Shadow in Japanese) is an evil organization with plans of world domination that it sets in motion during the course of Pokémon Colosseum and Pokémon XD: Gale of Darkness. The organization contains over 33 members, and countless Cipher peons.
The organization first appears at the beginning of Pokémon Colosseum, where Wes sees two thugs, later revealed to be Cipher members, carry off a sack after a supposed heist. The sack contains a girl, which Wes discovers on verturing to Phenac City, who has the ability to see the dark aura Ciper's Shadow Pokémon emit. After a short talk with the mayor op Phenac, Es Cade, Wes and the girl (Rui) venture off to defeat Cipher.
Most cities in Orre are either overrun by Cipher or controlled entirely by them: three of Cipher's four Admins: Miror B. , Dakim and Lady Venus control Pyrite Town, Mt. Battle and The Under respectively when Wes arrives at each. They took control through threats, covert means and outright violence. Agate Village is also terrorized by the group, with the goal to destroy the Relic Stone that allows Pokémon to return from its Shadow state.
Cipher's fourth administrator, Ein, serves as their lead scientist, and is the chief developer of Shadow Pokémon in a secret laboratory in the desert. Nascour is chief executive of the operation, giving directives to the admins, only appearing in person twice.
Team Snagem became partners to Cipher's plot: Snagem would steal Pokémon from Trainers, while Cipher would corrupt them into Shadow Pokémon. Cipher was the original developer of the snag machine stolen from Team Snagem by Wes.
With their Shadow Pokémon scheme nearing completion, despite Wes's snagging of the Shadow Pokémon he had encountered, Cipher builds Realgam Tower in the middle of the Orre desert, hoping to use its colosseum as a moneymaking venture where spectators could witness brutal battles between Pokémon who were fighting for their lives. With the intervention of Wes, this was prevented, and Nascour was defeated. However, at that moment, Es Cade arrives, revealing himself to be Evice, Cipher's true leader. He is defeated as well, and attempts to escape with a helicopter to avoid arrest, however, Ho-oh destroys the helicopter with a ball of fire, ending Cipher's scheme.
Pokémon XD: Gale of Darkness
Cipher returns in Pokémon XD, having refined their Shadow Pokémon creation and distribution techniques. Only Miror B. is present from the first plot; he, along with his minions, seeks to create Team Miror B. and collect Shadow Pokémon that Michael has failed to snag. As such, Miror B. is no longer affiliated Cipher.
All other members of the previous Ciper administration apparently are still serving jail time, with new administrators in their place. Lovrina serves as Ciper's new head of research and development, overhaulling Ein's techniques to create a Shadow Pokémon that is impossible to purify using the means present in Colosseum. Snattle serves as Cipher's plotter, while Gorigan is in charge of the Cipher Key Lair, where Shadow Pokémon are made en-masse.
Eldes and Ardos serve as bodyguards for Cipher's Grand Master, Greevil, accompanying him throughout the region as he tours in disguise as Mr. Verich. The two are Greevil's sons, with Ardos fully in support of Cipher's plans, while Eldes does not agree with many of their actions.
It is revealed in Pokémon XD that Evice was never the true leader of Cipher, implying that Greevil intervened after his defeat to crush Orre himself. It is possible that the wealthy old man mentioned as having made a fortune in The Under's mines is Greevil himself.
Pokémon XD: Gale of Darkness
- Hexagon Brothers
- Mirakle B.
- Folly (Formerly)
- Trudly (Formerly)
- Countless Cipher Grunts