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?

Impressed by Nanao Hibiya's skill with a sword, Kimberly Magic Academy instructor Theodore McFarlane saves the samurai from certain death amid a fierce battle. With his encouragement, Nanao enrolls in the academy, where she instantly becomes a celebrity after she and four of her peers save a student from an enraged troll. Under the leadership of Oliver Horn, a young man who seems to hide a troubled past, Nanao and her newfound friends start their magical apprenticeship at Kimberly—where only four out of five students make it to graduation in one piece. It does not take long for Oliver and his friends to experience the dangers of the academy firsthand, as a near-death encounter in the labyrinth under the school leaves Nanao grappling with her bloody past. The inexperienced yet determined students must stick together if they want to have a chance to survive and uncover the mysteries that the academy holds.

The story begins when the kingdom of Noigllado suddenly invades the small country of Azuelgatt and brings it to the brink of destruction. General Adnowell leads Noigllado's troops against Azuelgatt's final, remaining line of defense: the fortress Doroah, led by a skilled female warrior named Shamshir. (Source: ANN)

Following the destruction of the magical floating device from OVA 1, the Magic Academy falls to earth, but unfortunately lands on and breaks a demon seal, releasing hundreds of ancient demons into the forest around the academy. The teachers are barely keeping the demons away and are desperately searching for the pieces of the floating device, so to earn more magic stones, all of the students from Amelia's class decide to leave the academy (even though they were told not to) to find the missing pieces. (Source: ANN)