Jaden Yuki arrives late for the duel academy entrance exams. The principal insists he be given a chance, the Vice Princpal reluctantly agrees. He doesn't want Jaden there, and uses his own personal deck for the exam, to get rid of the late comer
Crowler fakes a note from Alexis and puts it on Jaden's shoes. Syrus finds the note, Jaden placed his shoes in Syrus's locker, Syrus goes to meet Alexis. Jaden goes after Syrus. When they find Alexis, she says could report them for being out after hours, but says if Jaden beats her in a duel, she won't report them.
The Academy receives a shipment of rare cards. Crowler gives Chazz the rarest/most powerful cards from the shipment and arranges for Chazz and Jaden to duel during the exams. How can Jaden win against Chazz's stacked deck?
Jaden and his friends hear a scary story about the abandoned Obelisx dorms where several students mysteriously vanished. Intrigued they set out to find the abandoned dorm. There they encounter a person who claims to be a shadow duelist, he's wearing the "Millenium Pendant" which looks suspiciously like the Millenium Puzzle. The shadow duelist has captured Alexis, he'll release her if Jaden defeats him in a Shadow duel.
Crowler knows Jaden and Syrus were in the abandoned dorm. They're informed that they have to duel as a team in a tag team duel. If they don't win the match they'll be expelled. In order to prepare for the duel, Jaden and Syrus duel against each other. During the duel, they'll learn about each other's strength's and weaknesses.
Chumly has been at the academy for years, his family believes it's time for him to come home. His father arrives to take him away from the academy. He offers Chumly one last chance to remain at the academy, if Chumly can beat him in a duel.
After Chazz's latest defeat by Jaden, Crowler begins to doubt Chazz's dueling ability. He has Bastion duel Chazz. If Chazz can defeat Bastion he's still worthy. If Bastion wins, he'll be offered a place in Obelisx blue.
When someone is stealing from the Card Shack, Jaden and the crew go on a steak out to catch the culprit, but when the thief turns out to be a former student who's been living in the jungle, a truly wild duel ensues.
Bastion believes he's finally figured out a way to defeat Jaden. Bastion and Jaden duel in front of the entire school. Bastion has found a way to prevent Jaden from summoning some of his most powerful cards.
Chumly's dream of becoming a card designer might be coming true. A card he designed has been accepted by Pegusus' company. He just needs a recommendation from the school to get the job. To do that he has to face off against the Vice Principal.
The top graduating student gets to pick his opponent for an end of school year duel. Zane asks Jaden to duel with him. The duel doesn't go as well as Zane hoped, Jaden doesn't seem to be dueling in his usual style.