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The player first meets Pegasus when confronting Bandit Keith for the second time. He takes Keith's place as the player's opponent and challenges him to a Shadow Game. After being defeated, he and Keith retreat, and the player obtains the card pack for winning the Beginner Cup.
During Noah's event, Pegasus roams the second map and can challenge the player to more Shadow Games if he is not going after members of The Big Five.
After Noah and Gozaburo are defeated, Pegasus is revealed to have been brainwashed by Noah. He becomes a friendly opponent towards the player and challenges him to normal duels, and can be found in the first map.