Since the final battle against GARDE's elites, Shobu Kirifuda and his friends were having a peaceful everyday life, filled with nothing but fun duels. But things did not last as during an expedition to Antarctica, Xanadu, one of Zakira's elite was revealed to be an impostor and starts killing all remaining members of GARDE and abducted Zakira, leaving Ash to escape and desperately asks for Shobu's help. As Shobu and his friends faced many hurdles in order to save Zakira, the truth begins to unfold as Adam, the first-ever Duelist in the world, is finally resurrecting from his long slumber.

The story of Star Cross is the final chapter of Shobu's adventure, and consists of him stopping a new enemy—Adam, the first Duelist of the world who desires full annihilation of mankind.