A mysterious organization is interested in fledging duelist Shobu Kirifuda's ability to bring Duel Master creatures to life. With the support of his friends, Shobu duels with passion, discipline, and heart as he strives to be like his father and become the next Kaijudo master.

The story centers around the card game Duel Masters, which revolves around five civilizations (Fire, Water, Light, Darkness, Nature).