Jaden is promoted to the second year. A gentle new student approaches into a duel with Jaden. The deck of the new student isn't powerful because it is created suddenly without preparation by the immediate purchase of 8 packs-40 cards-at a stand. By Large Angel Zaret, Jaden's life points are lowered to 1200. Syrus and the others have realized that the new student is actually a prominent duelist, Aster Phoenix.

Chancellor Crowler approaches Chazz nad tells him that Chazz can enter back into Obelisk Blue if he can defeat a new student called Reginald van Howell, or Reggie. Chazz accepts these conditions and the next day he and Reggie duel. Once, he was on the top class, but now he is in the Red dorm. Reggie can break through Chazz playing Ojama monsters. Although Chazz can do the first attack well by XYZ combo, it is striked by Gilford the Lightning and other monsters in soldier family deck. However, he isn't perturbed, looking through the competition during the past year. Then he uses Mega Ojama King.

Tyranno Hassleberry, the top first grade of yellow challenges Jaden for a duel. Tyranno was the original school gang leader, beating Jaden to prove the fact that the academy has charisma. He loves Dinosaurs, so he uses Dinosaur deck. By the field magic Jurassic World, Dinosaur and Beast families can be powered up, and even the trap is repulsed. Furthermore, by Ultra Evolution Pill Jyooshin Kayaku, Jaden is threatened by the evolution of Archaeopteryx to Black Tyranno with 2900 attack points.

The news about the promotion to yellow dorm has come to Syrus. Crowler has prepared the condition that he has to duel and defeat the girl called Missy of Blue dorm. Thus, Syrus becomes so frightened that Jaden and his friends have to encourage him. Syrus is playing Bigroid deck while Missy is fighting by an insect deck. Missy multiplies the number of ants on Syrus's field in oder to increase the attack points of Insect Princess up to 2900. On the other side, Sho is fighting without Power Bond, fusing three Bigroid to summon Drillroid

Jaden and Bastion are still Duel Academy students, so they have to practice a lot. Bastion uses his WaterDragon again, but Water Dragon can not defeat Jaden's ShiningFlareWingman. Before dueling against Zane, Aster talks to his manager about the future and his victory. Jaden is extremely surprised, when he sees Avian's appearance on Aster's field. During next turn, Aster fuses Avian with Burstnatrix, but instead of FlameWingman, Aster creates PhoenixEnforcer which impresses Jaden and Syrus. But the best thing in PhoenixGuy is that he can not be destroyed in battle. And thanks to that special ability, Aster defeats Zane, by fusing PhoenixEnforcer with Sparkman to summon ShiningPhoenixEnforcer and using DestructionOfDestiny to send 4 more ElementalHeroes to the graveyard and raise ShiningPhoenixGuy's attack to 4900.

Which side is using the true Hero? The conclusion is needed. Thus, the duel between Jaden and Aster has finally started. Jaden initiates the attack by Flame Wingman. Suddenly, Aster summons Phoenix Enforcer by the same fusion. Both of them are hitting each other at the same time. Also, the fight becomes the high-class Elemental Hero fusion battle between Shining Flare Wingman and Shining Phoenix Enforcer. Anyway, Aster hasn't approved Jaden having the talent as a Hero.

The duel between Jaden and Aster is continued. Using the field magic card The clock Tower of the Secluded Prison, the passage time of destiny is cut off strangely. Furthermore, D-Hero Destiny Hero? series monsters are summoned one after another. This leads Destiny. compared to the Elemental Hero monsters, to control the time freely. Many monsters of Jaden are destroyed while his several turns are thrown away. When he is going to revive, he suffers from the damage of the enemy's combo. Finally, The D-Hero confined in the Clock Tower appears.

After Jaden is defeated by Aster, his cards become invisible in white paper. On the other side, because of Dr. Crowler, Atticus approaches into a duel against his younger sister, Alexis. Atticus invites Alexis to join him in the sibling debut in the entertainment world. Atticus activates the field magic Ultimate Stage Clothes that can increase the attack points of a monster by 3000. However, the cloths are too large. That makes the movement become awkward. Thus, when he strikes, the attack of his monster isn't as powerful as it has the original attack points. Alexis is opposing him by the ritual monster, Cyber Angel series.

A mysterious guy, Sartorious, appears in front of Chazz and duels with him. Sartorious places his cards on the table face down, shuffles Chazz's deck, and says that the destiny of Chazz will be forseen through a card pulled out. That's how he duels like a Tarot. The Hangman's effect is shown according to its normal or reversed position. This becomes the confrontation between Saiou who can absolutely make the destiny and Chazz who opens his own destiny personally.

A disappointed Jaden wanders around outer space. It's weird, but with a friendly dolphin-shaped space alien's guidance, Jaden is reunited with an illustrated card he drew in his childhood, which Kaiba Corp. launched into space. But, that card became perfect by evolving through the power of space's intention. Jaden duels a hostile alien life form. At the end of the universe, the energy form obtains the power of Neo Space, and Jaden starts to understand a new deck concept that gives his monsters a power up.

The Ra Yellow Head, Professor Sartyr, tries to bring Sargent Hassleberry, who usually enters Slifer Red dorm, back to Ra Yellow dorm by using curry. Thus, the duel between Hassleberry and Sartyr begins. Will Hassleberry's platoon of dinosaurs win this war? Or will Sartyr have the sweet taste of victory with his curry-themed deck?

While Jaden is still away, Syrus and Tyranno have a quarrel over who should get the tile of Jaden's sworn brother. Thus the duel between Syrus and Tyranno which bet by the strong through towards their Big Brother begins.

After Zane is defeated by Aster in Pro League, his glory seems to be gone. He is then invited by an untrustworthy sponsor to join the underground duel. It is the duel to show the elements with desparate effort in front of savage audiences. Then the duel between Zane and Inukai begins.

Jaden, who is getting lost in the forest, becomes hungry and fades, reminding himself of his duels in the past.

Jaden has finally returned after leaving for a long time. He battles against Aster, betting by the abolition of Slifer Red dorm.

The duel between Jaden and Aster is continued.

Vice Principle Bonaparte has an argument against Temp. Principle Crowler about the abolishment of Slifer Red. Thus, the teachers duel begins.

Chazz beats one Obelisk Blue Student one after another, and preforms the unknown action of dying the entire Blue Dorm White. It is said that it is the "Association with the Light" which Sartorious commands that should be what a school dedicates themselves to. He Duels Alexis.

The Society of Light sends Chazz and Alexis to call Lorenzo to duel Jaden. Alexis tells Jaden that he should meet her in a duel dome/museum. Everyone thinks it is a date, but instead of a date, the member of the Society of Light, Lorenzo challenges Jaden to a duel.

The top rank pro duelist X is sent by the white association, approaching into the duel against Jaden.

In oder to verify Nabukabu Power, Sartorious predicts by his Tarot, comes to Duel Academy, and approaches into the duel against Tyranno Hassleberry.

In order to decide the destination of the study trip, Jaden approaches into the duel against Sartorious' representative Rose.

Duel Academy has the school trip to Domino City. It's the sanctuary duel place of Yugi Muto, Seto Kaiba, and others. Jaden and his friends visit Yugi's house and meet Grandpa. While walking into the town, Grandpa is kidnapped. Two assassins of The Society of Light, Thunder and Frost, chase after them and approach them into a tag duel.

The tag duel between Syrus/Tyranno and Thunder/Frost is continued.

Seeing Sartorious's sister Saleena, T-Bone becomes frantic to beat Jaden. Without knowing Jaden's face before, he joins a camp Slifer Red. Jaden and T-Bone don't know each other, but they finally become good friends. When they are going to duel, they realized their actual hatred against each other.