Jaden Yuki (manga)

In the manga, Jaden played a Deck similar to that of his anime counterpart as a child. While in the hospital for breaking one of his bones playing baseball, fellow patient Koyo Hibiki gave the boy his own nature-themed Elemental Hero Deck after he beat Jaden in a Duel (which included "Winged Kuriboh"), and as a result of the meeting with Koyo and his sister, Midori, Jaden was inspired to become a Duelist. From the outset of the manga storyline, he is already a student of Duel Academy, with Koyo's heroes standing by his side.

In the manga, Jaden's first Duel is not against Crowler (though it is mentioned) but against a Duelist named Mr. Ryuga, who tried to become a teacher by taking cards from defeated students, including Syrus. Enraged by this, he challenges the trainee teacher and wins even without the use of Spell Cards (Ryuga was cheating by using a ring that disabled the Duel Disks ability to read Spell Cards). He then goes onto challenge or be challenged by Chazz Princeton, Bastion Misawa, Alexis Rhodes and Syrus Truesdale. Jaden take part in the main tournament of the series, where he loses to Chazz in the finals. Although he defeated Chazz earlier in the manga, Chazz was able to overcome him in the rematch.

Following his defeat to Chazz, Winged Kuriboh led Jaden to the Abandoned Dorm, where he found Midori Dueling Mackenzie. Seeing Jaden, Midori attempts to comeback from a duel she was going to deliberately lose but is unable to win by that point. After the Duel, Jaden is powerless to save her from succumbing to the shadows. However, Jaden is able to defeat Reggie in a Duel, freeing her from the influence of Tragoedia and reviving Midori. Jaden seemingly ceases to use Koyo's Heroes after this Duel, and instead uses a Deck of his own design containing the "Masked Hero" series, though he does retain "Winged Kuriboh".

His first on-panel use of his new Deck is in a losing effort against Aster Phoenix and his "Vision Heroes". Jaden is later challenged by Adrian Gecko, whom Principal MacKenzie promised to promote to the Pro League should he defeat Jaden. Despite Adrian's use of the Legendary Planet "The Despair Uranus", Jaden ultimately defeats him. Immediately after this, he is confronted by Atticus Rhodes, who is under the full influence of Tragoedia. Jaden antes "Terra Firma" and "Winged Kuriboh" against the restoration of Koyo's health. This backfires, as Atticus defeats him with a combination of "The Suppression Pluto" and "The Eye of Truth". With that loss, Tragoedia absorbs his missing heart from the spirit of Winged Kuriboh, but the spirit narrowly saves Jaden from the Penalty Game beforehand.

Jaden and Chazz confront Tragoedia at the warehouse by the docks, and they Duel as a team against him. Though they gain an early advantage, Tragoedia comes back with a wide array of cards that he designed himself. . Pushed into a corner, Chazz leaves Jaden his face-down "A Hopeful Future", knowing the outcome of the Duel will be determined on the next turn. Jaden combines "Winged Kuriboh" with "Light and Darkness Dragon" to create "Ma'at", which lends its power to defeat Tragoedia. The spirits of "Winged Kuriboh" and "Light and Darkness Dragon" sacrifice themselves to seal Tragoedia permanently. Years later, after graduation, Jaden faces a revived Koyo for the world title.

Nature Elemental Hero
In the manga, Jaden uses an Elemental Hero Deck, different from that of his anime counterpart. The Deck once belonged to Koyo Hibiki, but Jaden had modified it throughout the years. Though he later switches to "Masked Heroes" as he felt that he dishonored Koyo while dueling Reggie MacKenzie, Jaden uses this Deck once more against Tragoedia, wanting to symbolically stand with Koyo to defeat the monster that put him into a coma.

Past Deck
Jaden used this Deck as a child to Duel his mentor, Koyo. It is similar to the Deck his anime counterpart originally uses.

Masked Hero
Jaden uses a Deck containing the "Masked Hero" monsters starting with his Duel against Aster Phoenix. These "Hero" monsters are capable of Transformation Summoning.