Jaden's limits are being tested by Professor Thelonius Viper because he was invited by Sheppard so he could improve the students' dueling. Many new faces from other Academies around the world show themselves, including Jesse Andersen, who, like Jaden, has the ability to speak to his Duel Monsters cards. 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. 

The season begins with the dinosaur-obsessed drill sergeant Tyranno Hassleberry joining the Academy. He joins the Ra Yellow dorm and quickly becomes friends with Jaden. Also arriving with the new students is pro duelist Aster Phoenix. Aster is later revealed to be part of an organization known as the Society of Light, who are out to take over the world. The true evil behind the Society begins to show itself, brainwashing the Academy's students, including several of Jaden's friends. At the same time, the "Genex Tournament" begins in the school, with students and pros alike competing. During the tournament, Sartorius, the leader of the Society of Light, gains control of a powerful laser satellite, with the power to brainwash the entire world. Jaden and the others work together with Aster Phoenix to save the world and free Sartorius from the evil that controls him.