Many years ago, the death of the emperor sparked riots and civil wars that ravaged Atlantia. Upon the throning of the young king Yaiba, treacherous rebels were executed to restore the peace the country once had. However, tainted by this radical act of governance, Atlantia continues to be enveloped under the shadow of oppressive rule.

Tsurugi Tatewaki is a spunky teenager who grew up in the rural countryside with little memory of his birth parents. One day in his home, he stumbles upon a mysterious sword that transforms into a Battle Spirits card. When armed forces from Atlantia confront Tsurugi with their sights set on procuring his card, the secrets behind Tsurugi's past seemingly begin to unravel.

Accompanied by a droid named Bringer, Tsurugi makes his way to the capital of Atlantia and encounters supposed warriors who wield similar swords. As his world is slowly turned upside down by the gradual appearance of greater mysteries, Tsurugi may have to question everything he knows, including his very own judgment on what separates good from evil.