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.

Serena, Sartorious' sister, guides Jaden, Aster, Grandpa, and Bastion to Kaiba Land. Aster and Jaden go inside the Virtual World to see Syrus and Tyranno as a Vehicroid and a dinosaur. Then Serena tells them that the only way that they can get out and save Syrus and Hasslebery is if they defeat her in a duel. The duel is also being held to see who is the chosen one to stand by Sartorious' side.

The unusual tag duel between Jaden and Aster VS Sarina is continued.

Dorothy is struggling to clean up Duel Academy before the rest of the school comes back and she notices that a doll has gone missing. The doll appears in a human form as a girl named Alice. Hassleberry falls in love with Alice and she carries him off to the forest. Jaden goes to the forest at night to investigate and then Alice challenges Jaden to a duel.

Bob, the quiz king who becomes attracted to Alexis, comes across Jaden having a quarrel against Alexis is forced into a duel with Jaden.

When all of the Ra Yellow students are entering the Society of Light, Bastion is upset that he isn't already part of the group. He says that since the Society of Light is for the best he should be already be a member. Bastion is so upset about the fact that he isn't a member that he goes to the White Dorm to challenge Sartorious. Instead of Bastion dueling Sartorious, Chazz is told to take his place and duel Bastion.

Zane, who is seeking for the sealed powerful deck, visits the former Chancellor Sheppard, and old master of Cyber Style Duel. Then, the student-teacher duel between Zane and Sheppard begins.

Chancellor Shepphard declares the opening of the GX Tournament. It's an important tournament that world Pro duelists and the students will participate in on Duel Academy Island. Sartorious then approaches to duel against a European champion, Prince Ojin.

Francis has appeared in front of Jaden. Pegasus and Chumley come from I2 Corporation urgently because the guy is an employee of I2 and a dangerous guy who uses a copy card of the greatest card "Winged Dragon of Ra".

Jaden is bored, having no opponent for this day of the Genex Tournament. Suddenly, a pro duelist, Orlando, appears in front of Jaden and challenges him to a duel.

Chazz confronts a pro duelist. He, who has become a member of Association of Light, applies "White Knights Swordsman" and obtains the victory with by such preponderant strength. Chazz confronts against Jaden, who was watching the duel, and demands the duel with him. Jaden is aware of the fact that there is no "Ojama Trio" in Chazz's deck. Thus, he decides to search from Chazz's important card- "Ojama Trio", and thinks of using it by himself to bring back Chazz.

Chazz continues his assault on Jaden using his "White Knight's Lord".

Zane returns to Duel Academy for the Genex Tournament and is asked for a duel by his old friend Atticus. Trying to use the shadows to save Zane, Atticus loses control over the shadows and Nightshroud returns for the duel.

Crowler and Vice-Principal Bonaparte are concerned about the reputation of the Academy due to lots students being beaten by pro duelists, so they decide to unleash their secret weapons to hopefully earn back the Academy's reputation.

The rumor about a duelist who participates in Genex and beats an opponent by one turn kill is spread out. The true identity of that person who makes a deal with The Grim Reaper's card is Lucien Grimly obtaining draw power. Jaden has to duel against Lucien whose soul has already been sold to The Grim Reaper.

While Dr. Crowler and Vice Principal Bonaparte get yelled at by Chancellor Sheppard, they take it the wrong way and believe that they got fired. This happens just as Pegasus, the president of the I2 Corporation shows up for a meeting with Chancellor Sheppard. Dr. Crowler and Vice Principal Bonaparte beg Pegasus to hire them and a duel is suggested to determine whether or not they will get the job.

Sartorious has two personalities against each other. One wants to conquer the world and make everybody "see the light". The other is the good side and is trying to stop the other side from achieving his goals. The good personality hands an important key each to Jaden and Aster. The evil side wants that key, so he sends Alexis to duel Jaden. Alexis' deck has become powerful with the influence of the light. Will Jaden be able to save Alexis?

Alexis' Deck, which was powered up by Sartorious, gradually drives Jaden into a corner. Jaden is fighting to return Alexis to her original self. However, Alexis, who isn't listening to Jaden, finally summons her strongest monster: White Knight Dragon. Jaden is pushed into a difficult situation, until he draws the card Chazz and Atticus entrusted him to return Alexis to her former self.

Syrus challenges his broher to a duel, hopefully to bring him back to normal. Zane accepts the challenge and the duel between the brothers begins. Syrus remembers what his brother had taught him about respecting the opponent. However, Zane forgets all he once knew,and taught to his brother, and attacks Syrus using his unique Cyber Tail Deck.

Sartorious, who has to recapture an important key, sends Dr. Eisenstein to confront Jaden. He is a genius medical doctor who creates a deck to counter Jaden's perfectly. The duel begins with the doctor activating Relativity Field and summoning a monster that can negate Jaden's skillful fusions, enabling him to quickly gain the advantage in the duel.

The real purpose of the GX tournament is revealed: Chancellor Sheppard and Pegasus searching for the person who posseses the Ultimate Destiny Hero card. As it turns out, Aster is also searching for this card. Meanwhile, Aster's legal gaurdian "The D" is about to avenge his title as world champion. However, "The D" has a secret important to Aster.

Aster learns that D is the one who stole the Ultimate Destiny Card from his father. He challenges D to a duel attached by a key entrusted from Sartorious. Aster begins the match with his D-Hero's, but the world champion proves a tough opponent even for Aster. D then activates the Ultimate D Card, pushing Aster into a tough spot. will Aster be able to beat D and finally find out what happened to his dad?

Jaden learns of the secret key from Linda, Prince Ojin's secretary. The key can activate the Laser Satellite. In order to retrieve it from Jaden, Sartorious orders Prince Ojin to duel Jaden. The prince is able to attack Jaden using three seperate Satellite Cannons. Jaden is able to call forth the Flame Wingman but is pushed into a tight situation.

Aster faces Sartorious to verify the words of his father that the Wave of Light clings to and enslaves Sartorious. Aster goes to the Society of Light's Private Duel Field, and demands answers from Sartorious. Sartorious, who took in the Wave of Light to the point it created another personality, has demanded Aster to return the key of the Laser Satellite to him. Aster's mind is made up, and begins his duel with Sartorious. Sartorious, who believes he's completely seen what Destiny has to offer, brings out the cards of the "Arcana".

Aster's Duel with Sartorious continues. Sartorious makes the 21st Arcana Force "The World" explode. Aster receives huge sums of damage, but believes inside Sartorious, despite being controlled by the Wave of Light, the "Real /True Sartorious" still exists. Against Sartorious's unwavering assault, Aster begins to give up. But something happens to allow Aster to begin his counter offensive strike. However, Aster succeeds at making "The Good Hearted Sartorious" appear finally.

Sartorious, controlled by the Wave of Light, has defeated Aster in their fight. Sartorious then demands Jaden's key to the Laser Satellite in exchange for Aster. Jaden's put in a pretty difficult situation. There is where Neos shows up to interject just as the key is about to go to Sartorious. Furious, Sartorious duels Jaden to put an end to things. Just like in his battle with Aster, Sartorious reads the future and becomes the dominant power in the duel. Despite this, Jaden summons his monsters through his specialty - Fusion.

Sartorius, controlled by the Wave of Light, activates the Field Spell Card [Light Boundary]. This Boundary has an adverse effect on the Card Spirits and Jaden's monsters are drove in it. Then, Sartorius summons Arcana Force [The World] and sticks it on Jaden. Meanwhile, Prince Orgene, controlled by the evil Sartorius, obtains two keys for the Laser Satellite and makes it mobile. Kenzan's already too late in his attempts to stop it, as the Laser Satellite has set it sights on Earth and fired just as planned....

Jaden summons Glow Neos and destroys the Light Boundary. With the tables turned in his favor, Jaden launches a direct attack on the evil Sartorious. In a jam, the controlled evil Sartorious sacrifices [The Material Lord], [The Spiritual Lord], and [The Heaven's Lord] to summon [Arcana Force Extra The Light Ruler], his ultimate card, to deliver a crushing blow. But Jaden Contact Fusions Ground Mole with Neos to summon "Ground Neos" to regain the counter offensive...