The world of Duel Monsters is once again evolving with the development of a network called Link Vrains and a new summoning mechanic introduced as Link Summoning. By using this cyberspace, duelists can now create their own avatars and duel their way to glory within a virtual reality.

However, much like the real world, the digital world is not free from war, conflict, and mysteries. Years ago, a hacker organization known as the Knights of Hanoi unleashed an attack on Link Vrains. Led by the anonymous Revolver, their aim was to annihilate the artificial intelligence program known as the Cyberse. After a failed attempt, one of their targets, Ignis, managed to escape and hide the Cyberse somewhere in the network.

Five years later, high school student Yuusaku Fujiki encounters a strange artificial intelligence program while dueling in Link Vrains. Under the guise of his avatar named Playmaker, Yuusaku and his partner in crime, Shouichi Kusanagi, decide to join forces with the peculiar existence. As he seeks the truth behind a mysterious incident of the past, Yuusaku battles against the Knights of Hanoi and SOL Technologies in a race that might alter the fate of the world.