Yu-Gi-Oh! GX takes place 10 years after Yu-Gi-Oh! The Duel Monsters card game has never been more well-known or well-liked. The protagonist of the novel, Jaden Yuki, hopes to improve himself by attending the Duel Academy established by Seto Kaiba. He encounters Yugi in a rush and receives a Duel Monsters card from him. This card of Yugi's is also immediately played during his admission exam, causing him to triumph in his battle. Dr. Cowler uses unscrupulous tactics, so he must defeat him to gain admission to the academy.
There are three alternative housing options at the academy: Slifer (Red), Ra (Yellow), and Obilisk (Blue). The players are placed to the homes based on their skill level and exam performance. Blue is the strongest and has a bright future ahead of them, whereas Red is the weakest and has only recently succeeded. A harmonious coexistence is nonetheless unlikely... In addition, Jaden does not exactly get along with the committee's chairman, the same Dr. Vellian Crowler. Jaden is not, however, by himself; he frequently goes on adventures with his pal Syrus and his monsters.