In The Falsebound Kingdom, when the player goes back to Yugi's story the second time, he will appear when the player defeats mission eight. He was waiting for Yugi, he tells Yugi about the past and then he joins the party. When Dark Magician Girl arrives late, Dark Magician was furious and told his student not to make any excuses. When Yugi ask who she was, Dark Magician says that she was a student called back from her training. He will ask Yugi to put her in the bottom of the roster.
In World Championship 2006, he appears as a Limited Duelist and he challenges the player to refer to September 2003 Forbidden and Limited Card List.
In World Championship 2007, he appears as a Level Three Limited Duelist and he challenges the player to only include Spellcaster monsters in the Deck. By beating him, the player gets closer to unlocking Level Four Limited Duelists and a new booster pack.
In World Championship 2006', Dark Magician plays a Chaos Deck entitled, "September 2003 Deck". In World Championship 2007, he plays a Spellcaster Deck entitled, "Believe in Magic!".