A Cipher Peon from Pokémon XD: Gale of Darkness
The organization first appears at the beginning of Pokémon Colosseum, where Wes sees two thugs, later revealed to be Cipher members Trudly and Folly, carry off a sack after a supposed heist. The sack contains a girl, which Wes discovers on venturing to Phenac City, who has the ability to see the dark aura Cipher's Shadow Pokémon emit. After consulting briefly with the mayor of Phenac City, Es Cade, Wes and Rui venture off to defeat Cipher.
Most cities in Orre are either overrun by the group or controlled entirely by them: three of Cipher's four administrators, Miror B., Dakim, and Venus, control Pyrite Town, Mt. Battle, and The Under, respectively, when Wes firsts arrives at each, having taken over the towns from their people through threats, covert means, and outright violence. Agate Village is also terrorized by the group, with the goal of destroying the Relic Stone.
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.
With their Shadow Pokémon scheme nearing completion, despite Wes' snagging of the Shadow Pokémon he had encountered, Cipher opens the newly completed 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. Near the top of Realgam Tower, Team Snagem's boss Gonzap unexpectedly arrives, and reveals a key truth behind the conspiracy: Team Snagem would steal Pokémon from Trainers, while Cipher would corrupt them and turn them into Shadow Pokémon. Cipher was the original developer of the Snag Machine stolen from Team Snagem by Wes. After defeating Gonzap, Wes enters the Tower's Colosseum and does battle with a gauntlet of Cipher agents at Nascour's behest, before finally facing off with the Cipher leader. Nascour falls in battle only for Es Cade to arrive and reveal his true identity as Evice, the real Cipher Head. Evice attempts to escape in a helicopter after being defeated by Wes, only for Ho-Oh to intervene and destroy the craft with Sacred Fire, bringing an end to Cipher's scheme.
Despite the organization's collapse, however, several Cipher agents continue to try and salvage their own plans in various locations. Gonzap also returns to the Snagem Hideout, where Wes defeats him again and prevents him from reorganizing Team Snagem. Once all the Shadow Pokémon are Snagged, including the Shadow Shuckle held by Cipher trainer Agnol in the Deep Colosseum, a Cipher Peon named Fein begins impersonating Wes, attacking citizens throughout Orre with his Shadow Togetic. With Togetic's capture, Cipher's plans come to a complete end.
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Cipher returns in Pokémon XD, having reorganized and refined their plans in the five years following the events of Colosseum. They are staffed by a new set of Cipher Admins: scientist Lovrina, who has perfected Ein's techniques for creating Shadow Pokémon; Snattle, the chief of Cipher's political arm; and Gorigan, the manager of the Cipher Key Lair factory producing Shadow Pokémon. The whereabouts of Dakim, Venus and Ein are unknown, while Miror B. has dropped out of Cipher to form Team Miror with Folly and Trudly. Aiming to steal Shadow Pokémon so they may ultimately capture all the world's Pokémon, Miror B. collects any Shadow Pokémon Michael fails to Snag during the game so they can be captured later.
Cipher makes their return in an attack on the S.S. Libra using XD001, a Shadow Lugia. A group of Cipher Peons led by Naps attacks the Pokémon HQ Lab shortly afterward to abduct Professor Krane, whose research on the Purify Chamber represents a threat to the organization's plans. Michael sets out to save Krane, in the process encountering a street thug named Zook and the mysterious Mr. Verich in Gateon Port, where Ardos, one of Verich's bodyguards, protects Michael and Jovi from Zook's Shadow Zangoose. Michael eventually discovers that Krane is held at Ein's old laboratory, which has been reactivated by Cipher. While searching the lab, Michael overhears the scientists talking about Cipher's leader Greevil visiting them, enraged over a failure of XD001's. After freeing Krane, Michael confronts Lovrina and defeats her, and the pair escape back to the lab with a Data ROM of Cipher's plans.
Krane dispatches Michael to Pyrite Town to meet with Nett of the anti-Cipher ONBS news network. Cipher attacks ONBS while Michael is off visiting Duking at the Poké Spots to recover the Data ROM, and Commander Exol has ONBS's servers wiped to prevent the information contained on it from leaking. This does not prevent Nett from learning that the Data ROM contained intelligence on a Cipher plot to attack Phenac City, where ONBS reporter Marcia has already gone. Michael travels to Phenac City only to discover that Cipher's operation has already begun, and most of the city's residents have been replaced with Cipher soldiers. In the abandoned Phenac Stadium, Michael finds Snattle holding Marcia and Cameran hostage, demanding they hand over their news footage, as it would damage his image as the governor Cipher intends to install to rule Orre when their plans are complete. Snattle's defeat is recorded by Marcia and Cameran and subsequently broadcast by ONBS as a warning to the region that Cipher has returned after their defeat five years ago. Michael, meanwhile, discovers the reason for Cipher's attack on Phenac City: the residents saw Cipher vehicles visiting a spot deep in the desert and engaging in suspicious activity.
Michael visits the site and discovers it is the S.S. Libra, dropped in the desert by XD001 following its hijacking. Gorigan and his men have been raiding the ship, kidnapping its Pokémon for conversion into Shadow Pokémon. After being sidetracked when the remnants of Team Snagem steal his Snag Machine, Michael pursues Gorigan to the Cipher Key Lair and infiltrates it with the aid of Gonzap and Team Snagem, who now oppose Cipher as well. At the top of the factory, Michael battles and defeats Gorigan, only for Mr. Verich to appear via video screen and reveal himself as Greevil, Cipher's Grand Master. Greevil challenges Michael to come to Citadark Isle, where Cipher's fortress is located, for a final showdown.
With the aid of Dr. Kaminko and his Robo Kyogre, Michael navigates the treacherous waters around Citadark Isle and reaches the facility, where he battles through an army of Cipher members as well as Lovrina, Snattle, and Gorigan. At the summit, Michael battles Ardos and Eldes, Greevil's bodyguards, before reaching the Grand Master himself. Greevil summons XD001 to do battle with Michael, bragging that it is the first of a planned army of Shadow Pokémon that cannot be purified, which Greevil intends to use to take over the world without having to rely on humans. Upon Michael defeating or Snagging XD001, Greevil attacks him in a rage, only to lose the subsequent battle despite having an entire party of Shadow Pokémon, including the legendary birds. Outraged at these events, Ardos demands that Greevil order the detonation of Citadark Isle to kill Michael, while they escape in a helicopter to resurrect Cipher elsewhere. Greevil hesitates, realizing that this would destroy all of their followers and data, but Ardos tells him such things can be replaced. Eldes intervenes and appeals to Greevil's humanity by addressing him as "father," enraging Ardos, who rejects seeing Greevil as anything other than the Grand Master, even further. His son's pleas get through to Greevil and he agrees to surrender to the police, but Ardos continues to refuse to accept this and leaves. Eldes approaches Michael and tells him that there will be no further threats from Cipher.
After collecting all of the other Shadow Pokémon, Michael tracks the last — a Dragonite stolen earlier by Miror B. — to Gateon Lighthouse and Snags it, ending the threat to Orre. The Cipher Admins go to Orre Colosseum and become professional trainers in earnest as they try to move on with their lives, with Lovrina intending to start her own fan club, Snattle continuing his ambitions to become governor through legitimate means, Gorigan becoming Michael's friend, and Eldes competing with Michael as a rival. Ardos, however, continues to refuse to give up on Cipher even as he battles at the Colosseum, swearing that he will one day resurrect the organization again and warning Michael that he will always be under surveillance as Cipher's biggest enemy.
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- Cipher has similar plans to Team Dim Sun in Pokémon Ranger: Shadows of Almia. Both of them have an undercover boss playing a major role in the region (Blake Hall as President of Altru and Es Cade as Mayor of Phenac City), both build a tower as part of their plans (Altru Tower and Realgam Tower), and make Pokémon lose their memories and effectively become mind-controlled slaves (Gigaremo units and Shadow Pokémon). Also, they are final bosses of their respective games, and can be re-battled at will.
- Cipher also has similar plans to Team Rocket. Both either stole Pokémon personally or were otherwise involved in Pokémon theft, both had plans for world domination involving Pokémon, both leaders also had a respectable and unassuming position in the first city visited by the player (Giovanni was the Gym Leader of Viridian City, whereas Evice/Es Cade was the Mayor of Phenac City), and both ended up being revived a few years later by someone other than their original leaders.
- Unlike other villain groups, Cipher is indicated to regularly use physical force on humans; during the kidnapping of Professor Krane and attack on the ONBS, Trainers are found injured on the ground, mentioning they couldn't stop Cipher, and during the attack on Phenac City, Cipher forces Justy to surrender by threatening hostages. In Pokémon Colosseum, it is shown that Shadow Pokémon do not hesitate to attack humans, which is also one of the possible effects on Shadow Pokémon in Hyper Mode.
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