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.

A strange shadow approaches Yuma, which turns out to be Tokunosuke Omoteura, a classmate of Yuma's known for his duplicitous tongue. In the morning, Yuma was reprimanded for a prank he pulled in front of the whole class that he has no memory of causing. As a result, he's been cut off from every one else. Tokunosuke gently says "Let's Duel". With "Baby Tragon" his new Xyz Monster, Yuma might enjoy this duel, but Tokunosuke seems to be planning something.

Tokunosuke steals Yuma's "Utopia", causing Astral to vanish. Tokunosuke had wanted the great power of Numbers, and Yuma tries to Summon "Leviathan Dragon" to fight back, but Tokunosuke's Trap Card takes even that away. When Yuma is pushed into a corner with his field, an unexpected monster will become the Trump Card of the Duel.

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.

A suspicious shadow is trailing Yuma. It seems someone has been after Yuma, and their identity is the unassuming girl Cat-chan from Yuma's class. Yuma and Kotori fall into Cat-chan's trap. To rescue Kotori, he's going to have to Duel. Astral is cautious of the strange vibes he's getting from Cat-chan, especially with the strategy of her "Transforming Cat Deck"!

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 his Duel with Shark, Yuma Duels Tetsuo Takeda without "Numbers" and loses twenty times in a row, with Tetsuo angry because Yuma lied about not using the "Numbers" against Shark. Yuma is scolded by Astral on his immaturity. On the other hand, Shark returns to "his place" where he gets involved in criminal company. Yuma, who knew what was going on with Shark, challenges the two strongest thugs: Rikuo and Kaio, to what Shark proposes to be a 2 on 2 "Tag-Team Duel".

Yuma finds himself pinned down by the overwhelming power of "Number 61: Volcasaurus". To protect their precious remaining Life Points, he defends Shark at his own expense. When their opponents summon their second Number monster at that point, Astral becomes aware of the hidden mysteries underlying the Duel. In a last-ditch effort, Shark notices Yuma's passion and entrusts him with 1 card that could turn the whole Duel around!

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.

Having clearly seen Kaito's power, and how utterly hopeless they are, Yuma and Astral are keenly aware that they cannot easily recover. At that time, Yuma talks to his grandmother. She mentions a mysterious old man named Jurou at a "Duel Lodge" who owns a wooden statue of the Legendary Monster "Dark Magician", who is waiting for Yuma and his crew. Yuma makes a strong wish based on his desire to train and get better!

It's a Duel against Jurou's former disciple, Yamikawa! Yamikawa draws his Ninja monsters, pinning Yuma down, but believing in the power of his friends, Yuma must continue this battle to the Death! But, Yamikawa summons his Trump Card, the Number Monster "Armed Ninja - Crimson Shadow"! However Yuma continues to believe in the power of his friends, but can this possibly lead him to win the Duel!?

Kotori and her friends, who are interested in the Number cards, plus Astral, form the "Number Club". To get more info about the Numbers, they visit the home of a fortuneteller, but the fortuneteller is under the orders of Kaito to collect the Number Cards! When the fortuneteller, Jin, kidnaps Kotori and the rest, Yuma and Astral come to the rescue, but the memory of their Duel with Kaito comes back, the visions of which continue to haunt them!

To save Kotori and the rest, Yuma continues to fight with Jin over the Numbers. Yuma's Life Points continue to fall, putting the fate of Kotori and the rest in a perilous situation, as Jin worsens things by summoning a second Numbers. In the midst of such a terrible pinch, Astral finds himself scared by Kaito's looming shadow, but when he sees Yuma who refuses to give up, he steps back up to the fight. With the feelings of these two guys, "Utopia" obtains a new power!

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.

Yuma safely recovers "Number 96: Black Mist" from a man. Tetsuo, who witnessed the Duel, takes note that Yuma seems suddenly more brutal in his strategy, and ends up in a fight with him. Not having reconciled in over 2 days, suddenly Number 96 swallows Yuma and Astral up!! To rescue Yuma and Astral from Number 96, Tetsuo fights the Numbers for the first time!

As they head home from class, Yuma and his friends meet Lilly whom they form a friendship with. However after the robot is reprogrammed to its former self, Yuma duels Lilly in order to help regain her memories.

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.