Juudai returns to Duel Academy, and a month goes by. Johan, O`Brien, Amon, and Jim return to their respective schools. Shou, Manjoume, and Rei move to the Blue Dorm and their new school lives start, but Juudai refuses to leave the Red Dorm, locking himself in instead. Amidst all this, a sudden malfunction occurs in the Duel System. Cards that don`t respond in Solid Vision begin to appear. To find the cause, Manjoume, Asuka, and Fujiwara Yusuke investigate the computer room. Meanwhile, Juudai receives a cell phone from an unknown sender, and with it, certain information.