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Set ten years after Yu-Gi-Oh!, GX follows a young boy named Jaden Yuki who, along with his friends, attends Duel Academy, a special institute founded by Seto Kaiba, in the hopes of becoming the next King of Games. Using his Elemental Hero deck and a Winged Kuriboh given to him by Yugi Moto, Jaden faces various challenges against other students, teachers and other mysterious beings.
For the first two years at Duel Academy, the main cast faces major threats including the Shadow Riders, who intend to revive the Sacred Beasts by creating a strong dueling presence on the island and obtaining the Seven Spirit Keys (held by Jaden Yuki, Zane Truesdale, Alexis Rhodes, Bastion Misawa, Chazz Princeton, Dr.Vellian Crowler and Lyman Banner) , as well as the Society of Light, which intends to enslave humanity with the mind control satellite of Misgarth. During the third year, Duel Academy is transported to another world–a desert plane with three suns and resident Duel Monster spirits–right into the hands of the Martin Empire. Upon returning home, Jaden and a select group of his partners dive into the rift left in their escape to recover their missing companion, Jesse Anderson, and embark through second and third worlds called Dark World. Jaden and friends meet up with an underground group that intends to fight the Dark World Order. During the duel that was Jaden vs Brron: Mad King of Dark World, Chazz, Hassleberry, Alexis, Ojama Green, Ojama Black, and Atticus are sent "to the Stars". After Jaden wins, he feels completely alone, and the spirit of the Supreme King takes over Jaden's body. Jim and Axel get sent to the stars trying to bring Jaden back to his normal self. Jaden overcomes his fear of the dark power that controlled him. During those very dark times, they find themselves face to face with the vindictive Yubel. When Jaden realizes the connection between Yubel and his past self, he uses Super Polymerization to fuse his soul with Yubel's, giving him certain powers. Jaden's exact words were, "I fuse my soul with Yubel's!".
In their final adventure, Jaden and his friends deal with the mysterious Trueman, a dark agent who copies the identity of his defeated opponents and seemingly wipes out their existence with them, trapping them in a nightmarish realm where they are mentally tortured by their personal failings. When a solar eclipse draws near, Trueman is revealed to be working for the real mastermind behind the vicious plot around the entire season - the former Shadow Rider, Nightshroud, using Yusuke Fujiwara as an avatar. Jaden and Jesse form a tag team to defeat Fujiwara and later Nightshroud himself in order to save the rest of the humanity from his World. After Jaden graduates, he is sent back in time in order to have an opportunity to duel with Yugi Moto.