After losing to Zakira, the young and passionate duelist Shobu Kirifuda realizes he must grow stronger and decides to leave for Spain to train. During his journey, he unexpectedly reunites with his father, Shori Kirifuda, who had been presumed dead for three years. Shobu soon learns of the legendary 7 Duel Masters, powerful duelists now scattered across the world. He resolves to find them, unaware that his nemesis Zakira has also begun his own search. Zakira deploys his elite team, the After-R (Revolution), intending to eliminate these formidable duelists and harness their power.

Shobu's quest becomes a global journey that takes him through various countries, leading to new encounters and emotional reunions. His path eventually forces him to confront a shocking enemy: an old friend transformed. Hakuoh, Shobu's former rival, has been brainwashed into a sinister alter-ego known as White, forcing Shobu to face him in battle.

The story unfolds across three major narrative arcs: the Spain arc, the Egypt arc, and the World Championships arc. The central conflict focuses on Shobu traveling the world to stop Zakira and the After-R from eliminating the world's strongest duelists. Key characters include the determined protagonist Shobu Kirifuda, his thought-to-be-lost father Shori Kirifuda, the villainous Zakira, the elite After-R squad, and the tragically brainwashed White, who was once Shobu's friend Hakuoh. The manga directly continues from the original Duel Masters series and serves as a canonical bridge to subsequent arcs featuring characters like Katta and Joe Kirifuda.