Haru Shirogane is a weak-minded person who is constantly bullied while Taiga has traveled from across the sea in hopes of becoming the strongest man in the world. One night, the two meet up with Shun Kamiya, the strongest XB (Extreme Baseball) player, and leader of the Minato Tribe. When they meet, each of the Tribes scattered throughout Neo-Tokyo are about to face a major threat. On the orders of the King of Neo-Tokyo, "Houtenshin", the Chiyoda Try, led by the mysterious Ojiro Otori, has started to take control of all the tribes in the country. Their evil clutches are about to reach the Minato Tribe...

In the ever-growing world of Duel Monsters, as duelists improve their skills and rise up the ranks, duels become increasingly complex. By adhering to strict rules, in addition to using and learning proven strategies, one can develop into a strong duelist. However, as a boy who loves inventions and discovering new possibilities, elementary school student Yuuga Oudou finds the current way of dueling predictable and rigid—in other words, boring. Thus, he aims to craft a new path in dueling with his exhilarating new invention: Rush Duels. His ambition soon catches the attention of Tatsuhisa Kamijou, a fellow elementary school student, who brings him to a mysterious place in an attempt to discover the potential of the new system. While Yuuga aims to implement Rush Duels as the new dueling standard and overthrow the conventions of the game, he opens the door to his ultimate goal—to make dueling exciting again.

Miyano spends his days peacefully reading Boys' Love comics and worrying about how girly his face is-until a chance encounter leads to a scuffle with his senior Sasaki. Intrigued by his feisty junior Miyano, delinquent Sasaki uses every opportunity he can to get closer...

The franchise's story is set in a world over a decade after futsal has skyrocketed in global popularity. Protagonist Haru Yamato watches the championship of the U-18 world cup and is inspired by a Japanese player named Tokinari Tenōji. He joins the Koyo Academy High School's futsal team with the goal of becoming a player like Tenōji. There, he finds friends, and together they face their rivals.