Set in the world where Modern and Fantasy exist one another. Yukato Hoshino eventually comes into a contact with a mysterious Primarch during a duel, only to find himself into the strange conflict as the existence of other Primarchs begins to run wild around the city of Atismata and his only goal is to exterminate them. But soon, the greater threat begins to arise elsewhere...

Set after the Two-Shot Prologue. The mysterious group known as the Omens have made their move along with a unknown Duel Spirit whose desire is to sow chaos. Yuji and his allies of the Agatsuma Team must deal with the unknown influence that infects them and find out just who are these Omens? What is their objective? And even that mysterious rival. The journey thus begins.