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Jaden and the player met at the Duel Academy entrance exam, to which they both arrived late. Vellian Crowler gave them both a second chance to enroll if they could defeat him in a Duel, and developed a dislike for both of them after his loss.
Jaden first duels the player one night after meeting Zane Truesdale at the Lighthouse.
When the player acquired their first Duel Spirit partner, Jaden informed the player that he was also able to see duel spirits and told them about his partner, Winged Kuriboh.
Crowler uses the player and Jaden's excursion to the Abadonded Dorm as an excuse to expel them, unless they can defeat a special pair of opponents that were to be announced and faced next day. Not feeling too confident, Jaden asks the player to edit his Deck before the Duel begins. The opponents are revealed to be the Paradox Brothers, who are faced separately - Jaden duels Dox, while the player is pitted against Para. Both Jaden and the player must win in order to continue the game.
Jaden duels the player at the Duel Field to decide Duel Academy's representative against North Academy.
As the last duel in the storyline, Jaden faces the player in the Duel Field again, this time in a Match, as the tournament's final match.
After beating the game, Jaden can be found around the Red Dorm, the entrance to Duel Academy and the forest.