After witnessing the dark powers of the Supreme King, Axel finds himself afraid for the first time in his life. Can Axel face his fears, or will the guilt of running scared force him to give up dueling for good?
Duel Academy's Graduation Duels begins, and Jaden Duels a second-year student named Daigo Sorano. Meanwhile, Trueman's attack begins in Domino City, where he begins absorbing residents into the World of Darkness.
Jaden is hallucinating, but begins to make his way back to Duel Academy. On the island, Trueman has taken the appearance and Deck of Daigo Sorano and is using them to defeat various students, continuing his siege, and absorbing people into the World of Darkness.
Jaden and Jesse continue their Duel against Nightshroud to save Yusuke Fujiwara. Nightshroud uses Trap Cards to manipulate the attacks and attributes of his opponent's monsters, while Jaden and Jesse narrowly avoid defeat after defeat.
Jaden appears to be the last remaining human on Earth, with only Pharaoh and the spirit of Professor Banner for company. Nightshroud reveals his true form, as well as the origins of the universe. Jaden and Nightshroud begin their final confrontation.
Jaden continues his confrontation with Nightshroud as the latter finds a way to counter Jaden's "Neos Wiseman". Those trapped in the World of Darkness begin to gain their memories and emotions back as Jaden attempts to find a way to prevail.
Jaden attends his graduation ceremony and ends up traveling back in time, where he Duels Yugi Muto when he was at his strongest - just after winning the Battle City tournament and acquiring the Egyptian God cards.