B-Daman CrossFire follows Riki Ryugasaki, a young boy who eventually discovers a particular game called, B-Daman. One day, he finds a B-Daman of his own named, Thunder Dracyan. Thunder Dracyan is inhabited by a B-Animal, mystical beasts trapped in the form of B-Daman figures.
Riki soon discovers how Dracyan's B-Animal is one of the Legendary Dragons, specifically the "Blue Dragon". His friend and rival, Samuru Shigane also owns one of these Dragons, the "White Dragon" in his Lightning Dravise. Together, they uncover a mystery and legend regarding these Dragons and plans by certain individuals seeking hegemony through them.
As a result, Riki and Samuru divulge themselves more into the sport of Cross Fight, learning the various new game types, mechanics and such while as they plan to thwart any B-Der wishing to rule the world. As simultaneously, they meet friends and enemies in what climaxes into B-Daman CrossFire