Yu-Gi-Oh! GX follows a young boy named Jaden Yuki who attends Duel Academy, a special institute founded by Seto Kaiba which teaches young duelists all about the game of Duel Monsters. Using his Elemental Hero deck and a Winged Kuriboh card given to him by Yugi Moto, Jaden makes various new friends and rivals and takes on many challenges in his quest to become the next King of Games. While not learning his lessons in class to make the grade, Jaden has proven that he is an exceptional duelist who can take on any foe. Together with his friends Syrus Truesdale, Chazz Princeton, Alexis Rhodes, and Bastion Misawa, Jaden takes on many different enemies that threaten the school. The first group was the Shadow Riders, a group that are composed of seven duelists of varying origins and backgrounds who each have their own agendas.
Then Jaden took on a group called the Society of Light. The Society of Light is a cult led by the alien-influenced Sartorius, the Society of Light’s legion of followers dedicates themselves to worshipping the Light of Destruction, intent on cleansing the Earth of its deficiencies. Sartorius is a fortune-teller with dual personalities under the influence of an alien force poised to remake the world in the image most befitting the extraterrestrial radiance within him. That plan soon failed when he lost to Jaden. Evil forces return to threaten not just Earth, but other dimensions as well, including the duel spirits' world. Jaden and his friends rise to fight this evil once again, but this time, the fight is more personal for Jaden. The "Supreme King" threatening the entire universe is actually a past incarnation of his, the dark side of his soul. Jaden soon finds himself facing the deranged duel spirit Yubel in a battle that will decide the fate of several universes, and takes the only path to defeat her, by absorbing her power into himself.
In the final story, Jaden is finally about to graduate from the Duel Academy, but a mysterious force starts its vicious attack, and it is up to Jaden to put a stop to it. Things are complicated further with the demise of several of Jaden's friends, and the return of a powerful enemy from the past. In the end, Jaden and his friends have safely made it to their graduation ceremonies. That evening, a thank-you party is held, but Jaden is nowhere to be found there. In front of him, who plans to pack up and venture out, Winged Kuriboh has appeared and led him to the exhibition gallery. There, Yugi Muto was waiting, and tells him that it's time to begin the real graduation duel.
Yugi informs a doubtful Jaden that Jaden has gained a lot of power over the past three years, but has lost something special, and that he must retrieve it. Once he holds his card over the deck, a timeslip to the world of the past comes from out of nowhere. Waiting there is Yugi from the past, which, by dueling him, will allow that special thing to be retrieved. The duel begins, and when the Duel starts heating up, Yami Yugi takes over the Duel, sensing that Jaden is a powerful opponent. Yami Yugi manages to summon some of the Egyptian Gods, but although the end of the Duel is never shown, it had concluded with Yami Yugi (Pharaoh Atem)'s victory. After the Duel, Jaden finds out that the thing he lost which was a passion for dueling. The show concludes with Jaden, Banner's spirit, and Pharaoh running into the distance, awaiting their next adventure.