The world of Duel Masters is one of five great civilizations. Through a card game, duelists can bring these worlds into existence, making what was previously abstract into reality. These skilled duelists are known as Kaijudo masters. Shobu Kirifuda is the best player at his local playground, and seeks to become a world-class master like his father. His first step on the road to conquest begins with winning a local tournament. Rather, it should have, except he is destroyed by the best Kaijudo master in the world, Knight. Shobu loses, but upon remembering the words of wisdom his father instilled into him, decides to continue on the road of becoming a duelist who can enjoy the game for what it is. And so begins his journey to victory－and as we all know, the journey is the most important part!

Shobu has returned after his 3 years training with all his friends in Battle Arena tournament. However, Shobu encounters a new enemy Zakira and his followers, the Fua Duelists. Zakira is a strong kaijudo duelist like Hakuoh. After kidnapping Hakuoh, they turn him into an enemy! Shobu and his friends try to stop them, but will they make it in time? Or will Shobu lose everything and end up devastated!?

It is featured in an alternate universe where Shobu had lost his duel against Hakuoh in their duel back in the Season 1 episode "Just Duel It". A mysterious organization is interested in fledgling 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 previous season of 'Zero Duel Masters' was set in an alternate universe, so this season's plot is a continuation of the Duel Masters Charge. It follows the aftermath of the duel of Shobu vs Zakira.

Shobu and friends fight the remaining Fua Duelists in order to defeat Zakira. Once again, they face off against the old members of Fua Duelists at the World Championship tournament. Shobu also found the terrible fate his friends faced because of these duelists in their past.