During the first year, Jaden plays an Elemental Hero Deck, composed of Spell and Trap Cards that support them, as well as his spirit partner "Winged Kuriboh". His deck largely supports Fusion Summoning stronger Elemental Heroes, often using a colorful array of Spell Cards, which have additional effects besides the aforementioned effect, allowing great flexibility in strategies. All Elemental Heroes fuse in some combination, granting Jaden a myriad of different effects to take advantage of. Some of his spell and monster card combinations serve as back-up strategies. His strategies are always full of surprises and he always draws the right card when needed.
Jaden continues to use his Neos deck in Season 3, debuting fusions involving "Elemental Hero Neos" and two, rather than one Neo-Spacian monsters as well as several new Elemental Hero fusions. In addition, the rest of the Chrysalis monsters make their debuts, as they had all been unseen save for "Chrysalis Dolphin", which was was used once in Season 2. After being freed from the influence of The Supreme King, Jaden keeps the "Super Polymerization" card, which proved to be one of the keys of ending his continued conflict with Yubel.
In his third year, while possessed by The Supreme King, Jaden plays an Evil Hero Deck, which consists of vile, more powerful incarnations of his regular Elemental Hero Fusions. As opposed to his flexible strategies that he normally uses, this deck consists of a much more straightforward approach that simply overpowers his opponents with the deadly effects of certain Evil Heroes, as his trademark card, "Dark Fusion", protects the summonedmonsters from being targeted by his opponent's effects.
After fusing his soul with Yubel, Jaden gains the ability to summon Duel Spirits in his own dimension. He usually uses this ability to summon Elemental Hero Neos, who is instrumental in saving Jaden's life more than once during the final Season. In this Season, cards that had not been seen since Season 1, such as "Mirror Gate" are included in Jaden's deck once more.
It's later revealed he still includes "Super Polymerization" in his deck and also uses "Yubel" herself. He's able to use the former to fuse the latter with "Elemental Hero Neos" to create "Neos Wiseman".
When Koyo decides to duel Jaden with his real deck, he tells Jaden to build the best deck he can. Jaden builds an Elemental heroes deck similar to Koyo's. This deck is very similar to the one his anime counterpart uses in the first year.
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