Es ist der größte Traum des dreizehnjährigen Yuma Tsukumo der beste Duellant der Welt zu werden. Ein ehrgeiziges Ziel, zu dessen Erfüllung es ihm leider an Talent mangelt. Als Schul-Rowdy Shark ihn eines Tages zum Duell herausfordert, erscheint plötzlich ein Wesen aus einer fernen Welt, das sich lediglich noch an seinen Namen, Astral, erinnern kann. Kurz bevor alles verloren scheint, schafft Yuma es mit Astrals Hilfe doch noch Shark zu besiegen. Fortan sind die beiden ein Team: Astral hilft Yuma dabei ein besserer Duellant zu werden und beide machen sich auf die Suche nach Astrals Erinnerungen, die in 99 Nummernkarten überall auf der Welt verteilt wurden.

Yuyu befindet sich im dritten Jahr der Mittelschule und ist partout nicht dazu in der Lage, die Bitten anderer auszuschlagen – dadurch wird er oft in die Hobbys seiner Schwester verwickelt. Doch er kann es nicht länger ertragen und läuft von zuhause weg. Kurz darauf wird er von Megumi gerettet, welche ihn in einen Nacht-Freizeitpark einlädt, in dem ihre Freunde abhängen. Der Park gilt als jugendlicher Treffpunkt der Gruppe „Team Blackout“, die dort Vanguard spielen. So wird Yuyu in die Welt von Vanguard hineingezogen und findet dabei neue Freunde.

Yuyu befindet sich im dritten Jahr der Mittelschule und ist partout nicht dazu in der Lage, die Bitten anderer auszuschlagen – dadurch wird er oft in die Hobbys seiner Schwester verwickelt. Doch er kann es nicht länger ertragen und läuft von zuhause weg. Kurz darauf wird er von Megumi gerettet, welche ihn in einen Nacht-Freizeitpark einlädt, in dem ihre Freunde abhängen. Der Park gilt als jugendlicher Treffpunkt der Gruppe „Team Blackout“, die dort Vanguard spielen. So wird Yuyu in die Welt von Vanguard hineingezogen und findet dabei neue Freunde.

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.