'''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.

* AbortedArc: The vs. Jack Rematch due to the tournament being interrupted. However the bonus chapter managed to fix that.
* AdaptationalBadass: In the anime Sherry was a BadassNormal but here she was made into a Psychic Duelist like Aki.
** The twins were able to defeat five duelists within the [=D1GP=].
** Yeager was made into a Riding Duelist here and he defeated nearly everyone in the second round of the [=D1GP=].
* AdaptationalVillainy: The twins Rua and Ruka first appeared as antagonists.
* AlternateContinuity
* BalloonBelly: Rua and Crow in a omake.
* BigBad: While all the signs point out the Skeleton Knight as this, in actuality it's really [[spoiler:Rex Goodwin.]]
* 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 regarding the monsters' names; not helped by the Duel Dragons having punny Japanese 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 first D-Wheel that Godwin uses in his duel against Jack looks the same as Jack's D-Wheel only darker in color.
** The Ultimate God's true form [[spoiler: looks exactly like the Crimson Dragon.]]
** [[spoiler: Holy Spark Dragon God - Stardust Sifr]] looks like Shooting Star Dragon but with six wings and the way it is summoned is similar to Shooting Quasar 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.
* AGodAmI: Rex Godwin, just like in the anime.
* GoldenSuperMode: [[spoiler:Stardust Chronicle Spark Dragon]]
* GreaterScopeVillain: [[spoiler:The Ultimate God]]
* [[IllGirl Ill Boy]]: Crow's younger brother Yoshi.
* InconsistentDub: Hoo boy. Even after TCG names are revealed, this doesn't mean that a card will stick to the name.
* 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.
* MythologyGag: Yeager's D-Wheel, the Destiny Clown is the same one from the video game Yu-Gi-Oh! 5D's Wheelie Breakers.
** Sherry's psychic ability, "Hand Scan" functions the same way as [[Manga/YuGiOh Pegasus's Millenium Eye.]]
** Two cards that are used by Yusei and Jack respectively in the bonus chapter are named after the MidSeasonUpgrade they received in the anime, [[http://yugioh.wikia.com/wiki/Accel_Synchro_(card) Accel Synchro]] and [[http://yugioh.wikia.com/wiki/Burning_Soul_(card) Burning Soul]].
* 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 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.