Twenty years after Glenmalt, the legendary Dragon Ruler, conquered the martial race known as Duel Masters, his twin children step onto the stage of a new era. The story follows Glenglassaugh and Glenturret, a sister and brother who carry the weight of their father's legendary status while forging their own paths. Glassaugh, the elder twin, grew up hearing tales of her father's battles and has nurtured a powerful dream to surpass him. Turret, her brother, was raised in the civilization of light under the care of his father's former rival, giving him a unique perspective that centers on the concept of love as a transformative force.

The catalyst for their adventure arrives when Miroku, a genius from the spirit world, appears and bestows upon them a mighty greatsword named Gaisaga, the Explosive Flame Greatsword. With this weapon, the twins enter the revived Duel Masters tournament, a no-holds-barred martial race that spans continents and offers the victor the chance to obtain whatever they desire. Miroku, fascinated by the Dragheart weapons that first appeared in the previous tournament, uses the event as a testing ground for his new creations.

The early portion of the narrative follows Glassaugh and Turret as they clash with a new generation of Draguners, warriors bonded to dragon spirits. Among their early rivals is Sasoris Jr., a childhood friend who becomes consumed by the power of another of Miroku's experimental weapons, the evil tomahawk Deadaxe. The twins must also contend with Q.E.Deux, a mysterious clone seeking to revive the ancient evil known as The Deadman, believing it will fulfill the wishes of her original self.

The middle of the story escalates dramatically with the invasion of King Romanov, the Purgatory Emperor. Having revived himself using one of Miroku's magical devices, Romanov sets his sights on obtaining Gaisaga. He attacks the twins directly, seeking to absorb all of history into his Evil Eye and ruling as a tyrant. This conflict forces the twins and their allies to confront a threat that even the villainous The Deadman considered a greater evil.

In the final narrative arc, the story expands its scope to depict the formation of two new factions: the Techno Samurai and the Steam Knight. As King Romanov's ambitions spiral into a larger conflict involving other powerful entities like Jashin and COMPLEX, the twins find their personal quest for glory intertwined with the fate of the entire dragon world. The conclusion of the Duel Masters tournament and the twins ultimate success in either surpassing their father's legacy or defining their own is reached, bringing this new chapter of the Dragon Saga to a close.