The player is on a ship, on their way to Duel Academy, with their friends Jaden Yuki and Syrus Truesdale. The player is placed in the Slifer Red dorm, and soon after, strange things begin to happen. As soon as these odd occurrences begin, you start hearing the voice of a duel spirit. This spirit is a good spirit and will help you duel and solve the mysteries surrounding the Duel Academy.