Yûma Tsukumo est considéré comme le « bad-boy » numéro un de son lycée et rêve de devenir un champion du duel de monstres. Un jour, Ryouga Kamishiro, un duelliste qui avait vaincu un autre élève, lance un défi à Yûma suite à ses provocations. Durant le duel, une lumière étrange apparaît, une entité connue sous le nom d'Astral… Une nouvelle aventure commence…
L'anime raconte l'histoire du jeune Sendo Aishi timide et distants tout aussi connus comme un le roi de la lâcheté ainsi qu'un imbattable roi du silence. Sa vie calme et silencieuse se verra chamboulé le jour ou son Blaster Blade une carte Vanguard qu'il a reçu d'une personne assez importante et qui devint au fil du temps l'objet le plus chérie par le jeune garçon. Il se le fera voler par un autre garçon de force. Ne perdant pas espoir le jeune garçon s'élance dans le monde des duels pour ne plus le quitter bercé par la sensation nouvelle que lui accorde se monde ou règne la volonté de l'imaginaire.
Yûyu Kondô, élève en troisième année de collège, est capable de lire dans le cœur des autres. Mais ceux qui connaissent son don, notamment sa famille, ont tendance à profiter de lui. Cherchant à fuir cet environnement, Yûyu fait un jour la connaissance de Megumi. Elle l’entraîne dans un endroit où se réunissent des joueurs Vanguard, notamment le groupe Team Blackout. L’adolescent est alors fasciné par ce jeu de cartes et la manière dont chaque équipe défend ses couleurs. Il se laisse convaincre de rejoindre ces nouveaux camarades...
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!
Bashin is a grade 6 student who loves trading card games. The globally popular card game Battle Spirits is all the rage. Through some strange circumstances, Bashin acquires a Pyroxene which gives Bashin the ability to become a Card Battler. He can summon the monster Spirits depicted on the cards so they can fight each other. Bashin learns that the legendary X Rare Card actually exists, and he engages in fierce card battles with other rivals to get the X Rare Card.
Dan is teaching young Battle Spirits fans about the cards, but he is suffering from a thirst he cannot quench. “I want fierce battles! I want to fight someone even stronger!!” And then Mai appears. She asks him to come with him to an era in which he can Battle. The new stage for Dan’s fights is the future. The Earth is being encroached on by Otherworld Mazoku monsters. He reunites with the administrator Kazan who asks him to rescue humanity from the brink of disaster.
In a new era of Battle Spirits, cards are treasures scattered throughout space. Adventurers called Card Questers battle against each other seeking out more and more powerful cards. The extremely tenacious Card Quester Rei and his beloved little dragon Mugen take off into the vast panoramas of space, blasting through the stratosphere of wild stars in the Star Number One. Rei masters various ultimate attributes, and transforms according to attribute colors!
Shunta, a boy who loves Battle Spirits, is led by a card and called to the “Spirits World” in another dimension. Eto, the priestess who summoned Shunta, warns of the Spirits World’s demise due to the evil God-King’s resurrection. In order to stop it, she says they must bring back together the twelve God-Kings for their powers. Joined by Yoku Albatrosa, a boy summoned from another dimension, Shunta is led by Eto on a journey to find the twelve God-Kings who are scattered throughout the world.
Two years have passed since the Mauve's uprising.
Gallet Revolt who has landed in Grand Lolo, following his battle with Vizarga has undergone great changes in his ideals. While in the "white world," Gallet meets a certain young man.
Meanwhile, Varte Parx, who rose as the leader of the Mauve, uses his aerial fortress to put pressure on the Unified Government. The confrontation between the Unified Government and Mauve continues to intensify.
Can Gallet change the future laid out in the Otherworld Records? The cogwheel of fate continues to rotate, and the world finally enters a time of change.
It is the year 2030, and the stage is the capital of Japan, Chou-Tokyo. Through "Buddyfight", humans have started cultural interactions with residents from other worlds called "Affinity Dimensions". Buddyfight is a game with selected humans as the "Buddyfighter", and residents from the other world as the partner (known as "Buddy Monster"). These battles have high significance and sometimes it is even used to decide the fate of a nation, and naturally there are those who seek to use the Buddy Monsters for evil purposes.
The year is 2661 CE. Ten years ago, Bashin Dan became the trigger that stopped the Earth from resetting itself. On the anniversary of this sacrifice, Barone and Clackey hold a conference, celebrating the union of Mazoku and humanity, and also Dan's feats.
However, beneath that peace, an organization named Cardinal Sign advocates for the subjugation of Mazoku and human supremacy. They resort to terrorist attacks, violence, and have somehow obtained the 12 Zodiac X-Rares which ought to have vanished together with Dan.
Amidst all this chaos, the bearers of the core's light feel a weird sensation, one that they've felt before. What could be the meaning of it, and what is the meaning behind the card that appeared within their decks, named "The Clash King's Miracle"?
The series follows the adventure of Bearers of Light's Core that will shape the destiny of the world.