In a place known as Den City, thousands of duelists take part in a virtual reality space known as LINK VRAINS, created by SOL Technologies, where users can create unique avatars and participate in games of Duel Monsters with each other. As a mysterious hacker organization known as the Knights of Hanoi, led by Varis, threatens this world, a high-school student and hacking genius named Yusaku Fujiki battles against them under the guise of Playmaker. Both the Knights and SOL Technologies are also after a peculiar self-aware artificial intelligence program, who holds the key to a secret area inside the network named the Cyberse World, which the Knights of Hanoi seek to destroy.
As the series begins, Yusaku sees the chance to capture this AI, which he names Ai, who sets off a digital maelstrom in LINK VRAINS known as the Data Storm. As the appearance of this storm gives birth to Speed Duels, in which duelists surf the wind as they duel, Yusaku battles against Hanoi in order to uncover the truth concerning an incident that happened to him 10 years ago. With the help of two Charisma Duelists, The Gore and Blue Angel, Playmaker is able to defeat Varis, saving the entire network and part ways with Ai who decides to return to his own world, the Cyberse World.