'''This work covers the manga. For the anime, see ''Anime/YuGiOh5Ds''.'''

Yusei Fudo is a powerful duelist living in Satellite. After having a friendly duel with his friend Sect Injuin, a mysterious being called The Skeleton Knight appears and kidnaps Sect forcing Yusei to duel the knight to save his friend. While heading to the hospital to help Sect who was injured in the duel, Yusei is attacked by Jack Atlas who forces him into a duel. Despite his best efforts, Yusei loses the duel and becomes frustrated due to his loss. Yeager appears and offers Yusei a chance to face Jack Atlas again by entering the D1 Grand Prix. Yusei wasn't sure about entering the tournament at first but he changed his mind after meeting Aki Izayoi. Yusei enters the D1 Grand Prix in hopes of getting another chance to duel Jack Atlas once more. However sinister things are happening behind the scenes...

Published in Shueisha's V-Jump in Japan and ''Magazine/ShonenJump'' in US before its cancellation, the manga is based off of the anime and although it features the same cast, the storyline is completely different.

The manga is written by Masahiro Hikokubo and supervised by Kazuki Takahashi.

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!!Tropes:

* AlternateContinuity
* BalloonBelly: Rua and Crow in a omake.
* BigBad: While all the signs point out the Skeleton Knight as this, in actuality its really [[spoiler: Rex Godwin.]]
* BiggerBad: [[spoiler: The Ultimate God]]
* BlackEyesOfCrazy: Duelists that are possessed by their Duel Dragons.
* DemonicPossession: Like above, Duelists can be controlled by their Duel Dragons.
* TheDragon: Sect under the Skeleton Knight's control
* DrunkOnTheDarkSide: See BlackEyesOfCrazy.
* DubNameChange: In the English version, all the main characters keep their English names but the characters that appear in the manga do not.
** Certain names that appear in the manga have been changed in the English version:
** Feel > Sense
** Dark Feel > Shadow Sense
** Purgatory > Void
** Card of Darkness/Dark Card > Shadow Card
** The Wizard of the Forest > The Black Magician of the Forest
*** InconsistentDub: Mostly to the monster's names.
* {{Expy}}: Six of the Duel Dragons look exactly like the Signer Dragons but with weird markings on their bodies.
** The Aerial Fortress Seibal is similar to the Ark Cradle.
** The Ultimate God's true form [[spoiler: looks exactly like the Crimson Dragon.]]
* EvilCounterpart: Underworld Dragon Dragonecro's monster effect allows it to create these.
* FauxAffablyEvil: Rex Godwin, as usual. While it's clear from the beginning, and even moreso during the first stage of the D1 Grand Prix, that he has some sort of plan, the true depths he's willing to sink to beat Skeleton Knight are made quite clear with [[spoiler: his willingess to MindRape Ruka and use her as a pawn to bring out Yusei's full potential]]
* FunWithAcronyms: V.S.F.L. (Virtual Soild Feel Lab). Changed to V.S.S.L. (Virtual Soild Sense Laboratory) in the English version.
* GoldenSuperMode: [[spoiler: Stardust Chronicle Spark Dragon]]
* [[IllGirl Ill Boy]]: Crow's younger brother Yoshi.
* InconsistentDub
* InTheHood: Ruka and Shinto Priest.
* MirrorMatch: Crow fights a dark copy of himself, the only difference between the two being that his copy has a Duel Dragon.
* RedBaron: King of Divine Punishment, Black Highlander
* ScarfOfAsskicking: Yusei wears one in Rides 9-12 during his duel with Bomber. He is also seen wearing it during the flashbacks of his TrainingFromHell.
* SinisterScythe: Black Highlander wields one.
* SoulJar: During the finals of the D1 Grand Prix, Yeager traps the souls of Duelists in cards.
* SuperMode: Four of the Duel Dragons have them, they are:
** [[spoiler: Demon King Super Dragon - Beelzeus]] for Beelze.
** [[spoiler: Dragococytus the Impure Underworld Dragon]] for Dragonecro.
** [[spoiler: Holy Spark Dragon God - Stardust Sifr, Stardust Assault Warrior, Stardust Charge Warrior, and Stardust Chronicle Spark Dragon]] for Stardust.
** [[spoiler: Burning Demon Dragon - Red Demon Abyss, Burning Demon Dragon - Red Demon Belial, and Burning Demon Dragon - Red Demon Calamity]] for Red Demon.
* TheCameo: Carly in Ride 9.
* TheReveal: The Skeleton Knight is actually [[spoiler: Rudger Godwin.]]
* UrbanLegend: The Skeleton Knight.
** AllMythsAreTrue: Naturally, he's real.