A mysterious organization becomes interested in the unique ability of a young and passionate duelist named Shobu Kirifuda, who can bring the creatures of the Duel Masters card game to life during his battles. The story is set in a world where the game is a deeply ingrained cultural phenomenon, and Shobu strives to follow in the footsteps of his legendary missing father, Shori Kirifuda, to become the next Kaijudo master. The card game itself is built around five distinct civilizations: Light, Water, Darkness, Fire, and Nature.

Driven by his love for dueling and his desire to reunite with his father, Shobu travels to the Temple to challenge the corrupted champion Hakuoh. After defeating Hakuoh and breaking the control of the sinister Master, Shobu continues his quest to become a true Kaijudo duelist. He confronts the evil organization P.L.O.O.P., which seeks to use creature civilizations to take over the world. Following these events, a more dangerous threat emerges in the form of Zakira and his Fua Duelists, who are searching for powerful Awakening Cards. Zakira successfully brainwashes Hakuoh into a new persona known as White, and in a devastating duel, Shobu loses his Awakening Cards, his friend Hakuoh, and his mentor Yakanman.

Refusing to give up, Shobu travels to Duel Island to grow stronger. The storyline continues in Duel Masters: Fighting Edge, where Shobu travels to Spain and Egypt to become more powerful and uncover the story of the seven Duel Masters. He is reunited with his supposedly deceased father and must stop Zakira and his elite followers, the After-R, from hunting down the world's strongest duelists. This arc forces Shobu to confront an old friend turned enemy: the brainwashed alter-ego of Hakuoh, now known as White. The canon timeline of Shobu's story concludes in Duel Masters: Star Cross.

After Shobu’s story concludes, the narrative focus shifts to his younger brother, Katta Kirifuda, in the Duel Masters Victory series. Katta later ages into an older protagonist in the Duel Masters Versus series. The legacy continues with the next generation, as Katta’s son, Joe Kirifuda, becomes the hero in the Duel Masters! and Duel Masters King series. The manga continues to follow the Kirifuda bloodline with the current series, Duel Masters Win, featuring a new protagonist named Win Kirifuda.