In Heartland, Yuma Tsukumo aspires to be the world's best Duelist. Despite this, he is not a good Duelist. When he ends up Dueling, Shark, a student known to have pro-level skills, odd things begin to happen and Yuma's story begins.

The Duel between Yuma and Ryoga comes to its conclusion. In order to take down "Leviathan Dragon", Yuma obtains a "Number" monster of his own, "Utopia".

Astral's been unable to leave since Yuma Dueled Shark, so, despite his reluctance, he's begun living with Yuma. At an inconvenient time, Akari Tsukumo has trouble when her PC she uses as a stay-at-home reporter crashes. When her big scoop is deleted as a result of a system down the city suffered, she orders Yuma to find an alternate scoop she can use for another manuscript. When Yuma goes into town, the traffic lights go nuts, causing downtown to fall into chaos. Yuma looks for the criminal who spread the computer virus that caused all this chaos.

Yuma challenges Professor Kitano, who is behind it all. Professor Kitano notes that each time he reduces his opponent's Life Points with "Electronic Computer-Beast Tera Byte" Astral's body weakens, causing him to slowly vanish! To make things worse, the Explosive Virus Time Bomb Ukyo has set is slowly reaching its countdown.

After having been around a while and having to work with Yuma, Astral's been fascinated by a TV Show Hero named "Different Dimension ESPer Robin". For some reason, Astral feels close and similar to this Robin from an alternate universe. One day, pictures show up with Robin in a fight downtown! Yuma, prodded by Astral, goes with Kotori to where the autographs were taken and meets Robin's actor, a kid named Fuya! But Fuya is a timid boy who doesn't resemble the Robin they all admire in the slightest.

The mysterious person posing as Robin around town was Fuya. Under the intolerable strain of being a hero, Fuya's heart has been dyed in darkness. Yuma challenges him to a Duel to save his soul. Robin, however, possesses "Number 83: Galaxy Queen". With it, he proceeds to summon one character after another from the TV Show. At first, Yuma and Astral were amused by this, but due to Galaxy Queen's almighty Monster Effect, they quickly grow impatient. To make things worse, Galaxy Queen, who currently possesses Robin, has taken on the appearance of Fuya's mother.

Yuma is reminded that his victories in his current Duels are due to Astral's help. To prove his skills, he fights Shark once more. Though Shark doesn't care to Duel again, he finally agrees when he finally reaches the end of his rope due to Yuma's constant following him around. The Duel of these two begins. Can Yuma win against Shark, who has no "Number" cards, when he himself declares he won't use his "Number" cards or require the aid of Astral!?

After a series of incidents, Yuma and Astral learn of the existence of a "Number Hunter". Astral remains wary of an unseen presence, but Yuma pretends not to care. As a result, a series of strange phenomena appear around these two. Undeniably, these are the signs of the coming of the "Number Hunter" named Kaito Tenjo. At that moment, a dangerous Duel with the Numbers cards on the line begins. With Kaito's power far beyond their reckoning, what can Astral or Yuma possibly do?

In just 1 Turn, Kaito Summons 2 Numbers. Yuma attempts to resist the onslaught, but all of his monsters have been removed from the field...! Kaito, capable of even more, summons the strongest Monster to exist: "Galaxy-Eyes Photon Dragon", which has never been seen before! Yuma summons "Number 39: Utopia" to create a turnaround despite the impossible odds facing him.

Yuma misplaces the the Emperor's Key that was an important momento from his parents. He and Astral look high and low for it, but they just can't seem to find it. While they look, Astral is curious as to how the Emperor's Key is related to Yuma's father. Yuma starts talking about various memories from his childhood that he remembers about his dad. Yuma's Never-Give-Up Spirit "Kattobingu" was born from a promise he made with his father.

In order to protect Yuma's Key from Kite, Shark faces him in a Duel.

While Yuma seeks for his Key, Astral duels against Kite to defend the Number cards he possesses.

Despite being unable to fight against the immense power of Galaxy-Eyes Photon Dragon, Astral, his resolve stern due to Feeling the Flow, continues a desperate combo of Offense and Defense. But when he finally gives up against Kite who keeps attacking him over and over, Yuma appears and the mysterious ZEXAL power activates...

One morning, Yuma heads to school, and while talking to his friends, time stops. He sees three suns shining in the sky. Together with Astral, they both shiver from a fear they do not understand, causing Yuma to run off to find out what possibly could have happened. At that time, Kite, using Dr. Faker's technology, retraces Astral's memories and invites Yuma to the World Duel Carnival.

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Quinton takes a timeout during his duel against Kite to reveal the long hidden mystery about Yuma's father's disappearance!

Quinton and Kite's confrontation in the cosmos comes to a climactic conclusion!

It all comes down to this! Yuma squares off against Vetrix in a battle that will determine the first ever World Duel Carnival Champion!

As the duel between Vetrix and Yuma races to its cataclysmic conclusion, Yuma stares down defeat and comes face-to-face with Vetrix's shocking secret!

This is it! The earth-shattering ending of Yuma's duel against Vetrix! Can Yuma rise above Vetrix's unrelenting onslaught, or will he meet defeat and lose everything he holds dear: his soul, his Numbers and... Astral?

Kite, Shark and Yuma join forces to take down Dr. Faker! Can this trio work together as a team and put an end to Faker's fury, or will Faker and his deck prove to be too much of a challenge for these three fearless friends?

With the fate of Astral World hanging in the balance, Yuma, Kite and Shark set their sights on stopping Dr. Faker, but before our three heroes can make their final move, Dr. Faker reveals the shocking reason behind his diabolical plan!

When a mysterious being from Barian World appears, Yuma, Kite and Shark must work together and battle like never before if they want to save Hart, Astral World... and themselves!

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The Barian invasion begins! Yuma faces a dangerous new enemy who will go to any extreme to gain possession of Yuma's Numbers in order to destroy Astral and his home!

Yuma's battle with a dangerous and powerful soldier of Barian World continues as he strives to keep Astral safe! Can Yuma beat this Barian enemy and his new Chaos Monster, or will Yuma end up losing what is most valuable to him... Astral?

When Yuma's buddies can't stop bickering, it's time for them to face-off in the Friendship Games, a sports dueling competition with surprises around every corner... including Barians!

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Astral and Yuma face a challenge so daunting that they must turn to their biggest adversary for help!

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