Synopsis
The Yu-Gi-Oh! GX anime began with Jaden, intending to attend Duel Academy, bumping into the protagonist of the original Yu-Gi-Oh! series, an obscure Yugi Mutou, on his way to the school's entrance examinations, being late and rushing. Yugi gave him a Winged Kuriboh card, which would become Jaden's signature monster during the first season and appear as a spirit guide. As he was late to the exam, an angry teacher, Vellain Crowler, duelled him for the practical entrance match using his own, powerful deck, instead of a school deck. Regardless, Jaden won the duel and was entered into Duel Academy. Jaden receives a low score on the exam's written component, and was therefore placed in Slifer Red, the lowest-ranked dormitory, alongside characters Syrus Truesdale and Chumley Huffington, who become his new friends. Early in the first season and out of spite, Crowler tried to kick Jaden out of school on many different occasions before finally beginning to respect him. However, he remained one of Jaden's rivals. After visiting an Obelisk Blue on-site duel arena by accident, Jaden met Chazz Princeton, an Obelisk Blue student who became Jaden's next rival. Jaden was shown to be an accomplished duelist, defeating the before-mentioned Crowler during his examination duel, Alexis Rhodes, who is hailed as the "Queen of Obelisk Blue", Chazz Princeton in a school-wide duel, and Bastion Misawa for the representative position in an inter-school duel, all three of whom received higher grades than he did and represented the higher-ranked dormitories.
As he was an accomplished duellist, the principal selected Jaden as one of the seven teachers and pupils to guard the Sacred Keys during the "Sacred Beasts" arc. Jaden defended his Sacred Key from the Shadow Riders, who intended to use the Keys to summon the powerful Sacred Beast cards, which were hidden at Duel Academy. Jaden eventually became the owner of the last Sacred Key. As such, he duelled the master of the Shadow Riders. Jaden won the duel and the Sacred Beasts were returned.
In the second season, Duel Academy had a new dormitory form, based on the Society of Light, an organisation of duelists focused on the Light of Destruction, a sentient being from another dimension that possessed a duelist named Sartorius. The Society of Light converted several of Jaden's friends and fellow students, making them worship the Light. Meanwhile, Jaden encountered Aster Phoenix, a duel champion who also used a HERO-themed deck. After losing a duel with him and being unable to see his cards, Jaden ventured into an extraterrestrial realm known as "Neo Space". He met the Neo-Spacians, cards he had designed for a competition as a child. Upon learning of an ongoing fight between the Neo-Spacians and the Light of Destruction, Jaden adopted the role of the universe's defender, wielding the "darkness of justice" against Sartorius and the Society of Light. He was charged with the task of rescuing most of his converted friends from the organization's clutches. Jaden was also entrusted one of the keys to the mind control satellite of Misgarth by Sartorius' good personality, and proceeds to purge the Light of Destruction from the diviner's body.
In the third season, Jaden was pursued by a deranged Yubel whose dedication to its mission had long since warped into a sick obsession with Jaden, where on many occasions it announced that it loved Jaden. After one of his friends, Jesse Andersen, sacrificed himself in order to defeat the deranged spirit, Jaden went on a rescue mission which forced him to confront his own feelings of inferiority and doubt. He succumbed to them, temporarily straying off the path of a hero by becoming the ruthless ruler of the third alternate dimension, the Supreme King. As Supreme King, Jaden dueled and collected the souls of numerous innocents to complete the Super Polymerization card, but was rescued by Axel Brodie.
Restored to his former self, Jaden confronts Yubel and taps into the power of Supreme King inside him to duel. Yubel then reveals that in a different dimension it was once a human who volunteered to become a monster to protect Jaden's past incarnation as a king until he became an adult, whose alter-ego Supreme King ( haou in the Japanese original) was destined to wield the power of darkness to keep balance with the Light of Destruction. Jaden, forgiving Yubel, fuses its soul with his soul with Super Polymerization, absorbing its powers and vanishing as the different dimension closes. Jaden returns to the original world after a wish on a falling star by Syrus results in Jaden crashing back to Duel Academy inside a meteor.
In the fourth season, Jaden has been fused with Yubel's soul, and its power occasionally manifests in the form of bichromatic eyes. He is also more serious and brooding, much to the confusion of the other members of the main cast. He is the only duel academy student still enrolled in Slifer Red. Jaden decides to leave Duel Academy, not wishing to put his friends in danger of a threat he feels gaining in strength. However, both Sartorius and Kagemaru attempt to convince him otherwise, believing that he is needed on the island to prevent a growing danger in the near future.
This seems to be well-advised, as before their meeting, Jaden already confronts a mysterious Obelisk Blue student by name of Yusuke Fujiwara, who can hypnotize people and set fires with his eyes, as well as a new darkness-controlling antagonist (or set of antagonists, as multiple copies of him are shown in the end of episode 158), Trueman, who seems to want both Jaden and Fujiwara dead. He also has to deal with the reemergence of Nightshroud, whose past may also tie into the mysteries behind Fujiwara and Trueman.
Later on the season, Jaden goes in a hurry to Domino City because Axel Brodie told him that it was empty, and that it might be a Trueman action. Jaden, however, gets there too late, and has to face Trueman, who had taken control of Axel. After Jaden is cornered by Trueman, Sartorius saved him and had a duel with him. Jaden later dueled Jesse, but due to the "Arcana Force 0: The Fool" card Sartorius had placed in Jaden's deck tainting his Polymerization card, Jaden believed he was facing Trueman. He eventually faces the real Nightshroud in a duel, and with the aid of Neos, the Neo-Spacians, and Yubel, manages to win. Now, on his Graduation Day, Jaden is challenged by the present-day Yugi, who indirectly takes him to the past for a true Graduation Duel against a younger Yugi.
Jaden duels against Yugi until the Pharaoh Atem takes over Yugi's body and summons Slifer the Sky Dragon. Jaden in return sends Neos into battle with the God Card. During his duel with Yugi and Atem, Jaden remembers the fun in dueling. It then pans to the desert. Jaden thanks Yugi for reminding him that dueling is fun. In the end, he is shown in a desert where he ends up traveling with Professor Banner's ghost and his cat, Pharaoh, towards the upcoming adventures.
In addition, in the Yu-Gi-Oh! Movie: Super Fusion! Bonds that Transcend Time he will work with Yugi and Yusei in the new movie by meeting with them through the powers of Yubel & The Supreme King. Jaden appears after Paradox steals Cyber End Dragon from Syrus & Rainbow Dragon from Jesse and begins to attack Venice. Though Jaden is able to defend himself with Elemental Hero Neos, Paradox soon attack Jaden & Neos with Stardust Dragon, a monster from the future, and overpowers Jaden. Before the final attack can connect, though, the Crimson Dragon appears and blocks the attack before disappearing and reveals that Yusei Fudo has followed the Crimson Dragon back in time to Jaden's time. Paradox soon takes his leave as Jaden explains to Yusei what Paradox's true intentions are: He plans to kill Pegasus around the time he was creating Duel Monsters, thus preventing the events of all 3 series from ever occurring & causing a time paradox. Using Crimson Dragon's powers, the 2 travel farther back in time to Yugi's time-era, only to be too late as Paradox has already come and gone, presumably killing Pegasus & Solomon Mutou, Yugi's grandpa, as well as stealing one of Kaiba's Blue Eyes White Dragon and Joey's Red Eyes Black Dragon. Yusei and Jaden manage to convince a grieving Yugi Mutou to help them stop Paradox and travel back to 30 minutes before Paradox's attack on Yugi's time. They manage to intercept Paradox and plea for him to stop, but to no avail. A 3-on-1 duel then begins, with Yugi, Jaden and Yusei sharing 4000 life points.
Though only having 1 turn in the duel, Jaden shows his mastery of fusion as he summons a new fusion monster, Elemental Hero Neos Knight, by fusing his Neos with Yusei's Junk Gardna and destroying Paradox's Sin Cyber End Dragon & Sin Rainbow Dragon. He & Yami Yugi also manage to convince Yusei, who loses faith in their victory after the summoning of Sin Truth Dragon, prepares to forfeit, instead to continue on and fight. He and Yami Yugi are able to give Stardust Dragon the power to defeat Sin Truth Dragon and defeat Paradox. Following their victory, all the damage Paradox caused to the timeline is repaired and our heroes return to their respective timelines with Yusei promising to protect the future & meet him and Yugi again.
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