The Battle Spirits Warring States Era is on rise. The Institution for Battle Spirits Administration (IBSA) has at least created a virtual system for spirits to battle in 3D. Thanks to this, the popularity of Battle Spirits has erupted all over the nation. All over, rivalries like that of local warlords have broken out between champion battlers. The battlers have but one objective, reach the top in Battle Spirits... Therefore unifying the nation. Now, the unification of this world will be risked with Battle Spirits... In this story of heated battlers... Who charge through this world of war.

Atlantia, the largest country of Legendia is torn apart by riots. 14 years later, a boy named Tsurugi Tatewaki, who was taken away from the chaos, meets Bringer, a card battler droid destined to protect Tsurugi. Tsurugi is trained in Battle Spirits to face the army of darkness, who is trying to gather the 12 Sword Braves to summon the Sword of Judgment

Hajime Hinobori is a grade 7 student who loves Battle Spirits. His parents leave him to research Battlefield Systems for the International Battle Spirits Association. Hajime is left under the care of their dear friend Dr. Denjiro. Then, Hajime finds a completed a Battlefield System demo machine. He will now fight as a Test Battler and is incredibly excited by the Spirits materialized in the Battlefield!

Shunta Mogami loves the Battle Spirits game. One day he is transported by a light from a Battle Spirits card to Spirits World, the origin of all Battle Spirits. He meets a girl named Eto, who claims to have summoned him to Spirits World in order to prevent its destruction at the hands of the revived Evil God-King, who once plotted the destruction of Spirits World before being defeated and sealed away. Together with the confident, green-deck-wielding Yoku Albatrosa, who also came from another world, Shunta sets out to find the twelve God-Kings whose power originally sealed the Evil God-King.