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Pokémon XD: Gale of Darkness is a game for the GameCube and is the sequel to Pokémon Colosseum. It features an adventure mode and a multiplayer mode. The adventure mode is an RPG where you assume the role of a young trainer called Micheal as he tries to stop Cipher from creating the ultimate Shadow Pokémon XD001 (Shadow Lugia). Whereas the multi-player mode consists of strictly battles against those with Pokémon Ruby Version, Pokémon Sapphire Version, Pokémon Emerald Version or Pokémon FireRed Version and Pokémon LeafGreen Version game paks.
The story begins 5 years after the events of Pokémon Colosseum with the introduction of Michael, the main protagonist. Michael first meets Professor Krane, his mother's boss and head professor. He introduces the problem of Shadow Pokémon (Pokémon whose hearts have been artificially closed). The criminal syndicate, Cipher is responsible for corrupting Pokémon and redistributing them as Shadow Pokémon with an aim for world domination. Krane also introduces the Snag Machine, which is used to legally capture Shadow Pokémon to purify them of their corrupted status. Krane gives Michael the responsibility to capture and purify these Shadow Pokémon and is given the Aura Reader, an eye piece scanner used to differentiate and identify them from normal Pokémon. Shortly after this, Krane is kidnapped by Cipher agents. Michael goes out to save Krane, purify the Shadow Pokémon and defeat the Cipher syndicate.
Michael travels to a Cipher base in the desert where he battles Cipher supporters, most of whom have Shadow Pokémon. Michael saves Krane defeating Cipher administrator, Lovrina in the process. After defeating her, a Cipher researcher drops a Data ROM, which Krane and Michael take back to the Pokémon HQ Lab to analyze. At the lab, the Purify Chamber is completed, as Michael and Krane return. Michael tests it out as Jovi takes the Data ROM to Datan, the scientist on the computer. Datan is no where to be found. After asking around Pokémon HQ Lab, he discovers him hiding outside. Michael finds out that Datan could not decode the data and would be embarrassed if Krane found out. A Krane overhears the conversation and sends Michael to Pyrite Town to give the Data ROM to Nett, a man who works at the news network for the Orre Region, ONBS.
Michael enters the ONBS main building. After performing various tasks, He gives the Data ROM to Nett, and leaves in search of a Pokespot, meeting Duking. The ONBS is then invaded by Cipher and the Data-ROM's contents are deleted.