In the fictional universe of Yu-Gi-Oh!, Duel Monsters, a popular card game created by Maximillion Pegasus (Pegasus J. Crawford) is widely enjoyed. Referred to as a "duelist," a player of the game summons monsters and activates Spell and Trap Cards through Duel Disk technology to evoke various strategies to defeat his/her opponent in battle. A Duel typically begins with each contestant being given a life total of 4,000 Life Points, which can be decreased as opposing players "attack" him/her with their monsters or trigger the abilities of individual cards. The objective is to reduce an opponent's Life Points to zero, and therefore be declared the winner. Although conceived solely as a card game, Duel Monsters' roots are mythological in nature, and many exploit its otherworldly secrets for their own personal gain.
Yu-Gi-Oh! GX begins 10 years after the events of Yu-Gi-Oh! with the lead character Jaden Yuki obtaining a Winged Kuriboh card from Yugi Muto, the renowned Duel Monsters champion, while on his way to a Duel Academy (Duel Academia in the original Japanese language version) entrance exam.
The Academy was founded by Seto Kaiba on a remote island in the Southern Seas, with its dormitories named after the three Egyptian God Cards, and is run by Chancellor Sheppard and his staff. The most elaborate dormitory, Obelisk Blue, is named after Obelisk the Tormentor. The Obelisk Blue dormitory can be graduated to, but the only way to enter the dormitory in the first year is to attend and do well at an affiliated junior school (English version only). As the highest ranked dormitory, Obelisk Blue's facilities are of the highest quality, on the level of the world's classiest hotels and restaurants. The center dorm, Ra Yellow, is named after The Winged Dragon of Ra. Those who were given the highest scores in the entrance exam, or who only did mediocrely in the junior school enter this dormitory, which, while not as extravagant as Obelisk Blue, still has incredibly clean and well-kept facilities and meals of a quality far above the lifestyle of the average salaried man. The lowest dormitory, Slifer Red (Osiris Red in the original Japanese language version), is named after Slifer the Sky Dragon. Those who failed completely or scored poorly are put into the shoddy quarters of Slifer Red.
There are four other branches of Duel Academy worldwide, in the North, East, South, and West. Most of the episodes only show Central Academy, although Northern Academy is shown in one episode.
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, and embark through second and third worlds where failure in duels sends losers to the stars ("killed" in the Japanese version, though they were actually sent to another dimension); in 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 fuses her soul with his, giving him certain powers.
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 then. 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, Nightshroud explains that Trueman's adversaries were trapped in the hell-like World of Darkness, where they will ultimately give up on their own lives because while in the dark world they would be mentally tortured by visions of failing at their hopes and dreams. 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. This concludes the Duel Academy senior's reign as students, and before the seniors graduate and go on their own separate paths, a farewell party is thrown. However, Jaden is not present because he dislikes sad events, and attempts to leave before anyone can notice he's gone. Before he leaves, Winged Kuriboh leads him to the room that holds Yugi Moto's legendary dueling deck, and he is encountered by none other than Yugi himself. They both are transported to the past, where Jaden duels a younger Yugi and in the process recovers what he had lost, his passion for dueling. The outcome of this duel is not known, but it's assumed Yugi is the winner given Jaden's promise to become stronger and duel Yugi again. As Jaden Yuki leaves, he discovers a note from his friends, who knew that he would probably attempt to leave early. The show concludes with Jaden, with Banner's spirit and Pharaoh running into the distance, awaiting their next adventure.