When Jaden arrives late to his entrance exam for Duel Academy he has to go above and beyond expectations to prove that he deserves to make the cut!

The incoming class is welcomed to Duel Academy, but Jaden finds a less than warm reception from freshman hot shot Chazz when he's challenged to a high-stakes duel!

Having been caught for trespassing into the abandoned dorm Jaden and Syrus are sentenced to a tag team duel where if they lose, they get expelled, so to prepare for the big match they decide to duel each other!

When a love struck girl sneaks into the boys dorm, Jaden challenges her to a duel to find out exactly why she's there and what she wants.

When Jaden and the gang get trapped in an ancient world it's up to Jaden to win a duel or be buried alive with the rest of his friends!

Jaden continues to battle in the duel of his life, finally winning his and his friend's freedom and just barely making it back to his world.

Finally, Jaden steps up to confront Camula.

Titan, the Shadow Duelist persuades Alexis to duel him to by promising to return her brother's memory is she wins--but if she loses, she'll be the one in need of rescue gaga.

When Chumley is accepted into Industrial Illusions card design program, he must beat Dr. Crowler in a duel to win his consent!

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.

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.

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

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.

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

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.

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

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.

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.

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.

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...

Jaden reflects on last year's adventures as he prepares for the third year at Duel Academy.

Syrus is kidnapped by Duel Academy's new bad boy Axel Brodie, and only Jaden can save him... by dueling Axel.

Jaden's duel against Axel continues as Syrus's life hangs by a thread... literally.

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Most of the students have returned from the alternate universe only to find that a few of their friends were left behind. Full of guilt, Jaden concocts a dangerous plan to get them back.

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