Yu-Gi-Oh! 5D's is set in the future in Neo Domino City. Seventeen years prior, a reactor called Moment within the city malfunctioned and caused a great earthquake that split the city in two parts: Satellite, the rundown and poverty-stricken part, and Neo Domino City, the wealthier and urban part, with access from Satellite to Neo Domino being strictly forbidden. Yusei Fudo, an aspiring duelist from Satellite, builds his own D-Wheel, but his best friend Jack Atlas betrays him and steals his vehicle along with his most precious monster, Stardust Dragon, escaping to Neo Domino. Two years later, Yusei builds another one and secretly travels to the city to win back his Dragon. Jack has made a name for himself and his monster, Red Archfiend Dragon, as the current Riding Duel King in Neo Domino City.
Yusei and Jack face each other in a Riding Duel, and Yusei is able to regain control of Stardust Dragon. As Stardust and Red Archfiend Dragon battle, Yusei and Jack's arms glow red, a third red dragon appears, and brings an abrupt end to the fight. This attracts the attention of Rex Goodwin, the head of the Public Security Maintenance Bureau, who reveals to Jack a five thousand year old secret, involving the "People of the Stars", a pre-Incan civilization, the "Crimson Dragon", and "Signers", identified by a red birthmark on their arm that represents a part of the dragon.
Goodwin also reveals that Jack and Yusei, along with child Duelist Luna and Psychic Duelist Akiza are descendants of them and are destined to face the Dark Signers, duelists resurrected from the dead to serve the evil Earthbound Gods. The Signers head to Satellite to face these foes who consist of: Rutger Goodwin , Kyosuke Kiryu , Demak, Misty Lola. After their defeat, Rex Goodwin is revealed to have become a Dark Signer and uses his brother's severed arm to become a Signer as well. Yusei, Jack and Crow then face him in a Riding Duel in order to stop him and the released King of the Netherworld from finishing off the Signers and destroying the world. Before the final attack, Yusei gains the Head mark while Crow gains his former Tail mark, making him a Signer. With the power of the Crimson Dragon and Yusei's Saver Star Dragon, he defeats Goodwin who, along with Rutger, sacrifice themselves to destroy the King of the Netherworld and revive the Dark Signers as normal people again.
After the Dark Signers' defeat, Neo Domino City and Satellite are finally reunited into one prosperous city with the building of the "Daedalus Bridge", an intricate net of roads linking both Satellite and Neo Domino City with some sections also used for Riding Duels. Yusei and his friends, now calling themselves "Team 5D's", prepare for the upcoming World Riding Duel Grand Prix tournament. A new threat appears, the Three Emperors of Iliaster, whose main monsters, the "Machine Emperors", can absorb Synchro Monsters from their opponents to empower themselves. Yusei encounters a fellow competitor.
Sherry LeBlanc, who is investigating the Iliaster organization, that is reportedly responsible for her parents' deaths. Team 5D's is also joined by a mysterious amnesiac mechanic named Bruno, whose secret alter ego Antinomy teaches Yusei about the secrets of "Accel Synchro", a summoning method that allows him to bring out an improved version of his Stardust Dragon. The WRGP soon begins, with Team 5D's facing tough opponents before eventually confronting the Emperors themselves, who are revealed to be three different incarnations of Aporia, a cyborg sent from the future to destroy Neo Domino City to prevent a great calamity from befalling mankind in the future.
Although Team 5D's defeats Aporia and wins the WRGP, a massive citadel known as the Ark Cradle appears and threatens to crash into Neo Domino City and destroy it. Team 5D's climbs aboard it to stop it. Before reaching the core of the fortress, they confront three individuals guarding its access: Aki and Crow face Sherry, who was promised to have her parents returned to her; Yusei faces Bruno, who recovered his memories of being Antinomy, another member of Iliaster; and Jack, Leo and Luna face Aporia. Lua dies during the duel and is revived by the Crimson Dragon, becoming the sixth Signer bearing the mark of the dragon's Heart.
When the Signers finally reach Z-one, Iliaster's leader, Yusei borrows his friends' dragons to add them to his deck, and challenges Z-one to a final Riding Duel to decide Neo Domino City's future. Z-one is revealed to be a scientist from the future who assumed Yusei's identity and traveled back in time to prevent the destruction of humanity. Yusei manages to use his friends' cards to perform a "Limit Over Accel Synchro" and summon his strongest monster, "Shooting Quasar Dragon". After Z-one is defeated by Yusei, he decides to entrust the future of mankind to Yusei, and sacrifices himself to destroy the Ark Cradle and save Neo Domino City from destruction.
A few months pass after the Signers' victory over Iliaster, and the former members of Team 5D's move on with their lives following separate paths. They all part ways, except for Yusei, who decides to stay in Neo Domino City and research for a way to stop the destruction of humanity in the future. The other Signers decide that they will return after fulfilling their dreams. As they ride together one last time, the Crimson Dragon removes their Signer marks, as their mission as Signers is accomplished.