Jaden Yuki is on his way to the Duel Academy entrance exams when he bumps into Yugi Muto, who gives him a special card, the Winged Kuriboh. Jaden hurries off to the exams, but arrives late. He is given one last chance to get into the Academy, but must first beat Professor Crowler in a duel. Crowler plays his best monster, the powerful Ancient Gear Golem, but Jaden is able to prevail using his new partner, Winged Kuriboh, and the power of his Elemental Hero deck.

A month has passed since the Yubel incident. Life at the Academy has started anew, but Jaden has stayed secluded in his room at the Red dorms. In the midst of things, something goes awry with the Duel System. Some cards stop responding to Solid Vision. Dallas, a new face everyone believes has been with them for years, examines the computer room and learns the location of the abandoned Obelisk Blue dorm. Meanwhile, Jaden has received a cell phone from an unknown sender and is told some enigmatic information.