Since the final battle against GARDES elite forces, Shobu Kirifuda and his friends have been enjoying a peaceful everyday life filled with fun duels. This tranquility is shattered during an expedition to Antarctica when Xanadu, one of Zakiras elite guards, is revealed to be an impostor. Xanadu attacks and kills the remaining members of GARDE, abducts Zakira, and leaves only a duelist named Ash to escape. Ash desperately seeks out Shobu to ask for his help. As Shobu and his friends travel to the frozen continent to save Zakira, a deeper truth begins to unfold. The first-ever duelist in the world, a being named Adam, is finally resurrecting from his long slumber.

The story of Star Cross serves as the final chapter of Shobus adventure. The central conflict revolves around stopping Adam, who desires the full annihilation of mankind. Shobu is joined by his rival-turned-ally Hakuoh and his friends Rekuta and Mimi as they face this new threat. The setting shifts from the characters daily lives to the harsh and mysterious environment of Antarctica, where ancient secrets of the Duel Masters world lie buried.

Several notable narrative arcs drive the plot. The story begins with the Antarctica Arc, triggered by Xanadus betrayal and Zakiras abduction, leading Shobu and his companions to embark on a rescue mission. Upon arrival, they encounter powerful giants and duel them, which inadvertently awakens Adam. A significant volume provides detailed events where Shobu and Hakuoh must build a combined deck to defeat two giant duelists in a tag duel, showcasing their teamwork. The narrative also features the revelation of an impostor named Shori and the intervention of a mysterious group. Ultimately, the events of Star Cross are considered canon to the Duel Masters timeline, leading directly to the arcs featuring Shobus younger brother Katta and Joe.