Obsessed with revenge against the King of Games, Seto Kaiba commences an excavation in Egypt to find the fragments of the Millennium Puzzle, which once retained the spirit of the "counterpart Yuugi." However, a cloaked man steals two pieces of the Puzzle and disappears before it could be reconstructed. Meanwhile, now in their final year of high school, Yuugi Mutou and his friends plan for their futures, unaware of the danger lurking close by.

Yu☆Gi☆Oh! The Dark Side of Dimensions tells the tale of vindictive forces distorting reality in whatever way they please. Will Seto and Yuugi move past their differences and save the world, or will Seto's own greed get the better of him?