Taking place six months after the initial Yu-Gi-Oh! manga, Yugi Muto and his friends are in their final year of high school and discussing their future plans. In the meantime, Seto Kaiba has organized an excavation to recover the disassembled Millennium Puzzle from the ruins of the Millennium chamber. The item used to hold the soul of his rival, Atem, who Kaiba aims to resurrect to settle their rivalry. Amidst the excavation, an unknown man challenges Kaiba to a game of Duel Monsters, steals two pieces of the retrieved Puzzle and leaves Kaiba wondering about his intentions. As the stakes increase, the rivalries intensify, and the danger grows exponentially.