Plot
''Yu-Gi-Oh! 5D's'' is set in the distant future, in Neo Domino City.
Seventeen years ago, Moment, a reactor within the city, malfunctioned and caused a great earthquake that split the city into two parts: Satellite, the former Domino City which is now the rundown and poverty-stricken part, and Neo Domino City, the wealthier and urban part. In order to keep the two areas separate, access to the city from Satellite is strictly prohibited and can result in imprisonment. Yusei Fudo, an aspiring duelist from Satellite, builds his own Duel Runner (D-Wheel in the Japanese version), 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 Duel Runner and secretly travels to the city to win back his Dragon. Jack has made a name for himself and his monster, Red Dragon Archfiend, as the current Turbo Duel King in Neo Domino City. As Yusei and Jack face each other in a Turbo Duel, their arms glow red and a third red dragon appears, bringing an end to the fight. This attracts the attention of Rex Goodwin, the head of the Public Security Maintenance Bureau. He reveals to Jack a five thousand year old secret, involving the "People of the Stars" (星の民), a pre-Incan civilization, the "Crimson Dragon" (赤き竜), and "Signers" (シグナー), identified by a red birthmark on their arm that represents a part of the dragon. Goodwin also reveals that Jack and Yusei are both Signers and holds a tournament to find the other three. Two of the other Signers turn out to be child duelist Luna and psychic duelist Akiza. In the final battle, the four Signers see a vision of the future with Satellite in ruins.
Goodwin reveals that the Signers 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 the Dark Signers, which consist of Rex's brother Roman Goodwin, a former Signer with the dragon's Head mark and leader of the Dark Signers; Kalin Kessler, a former friend of Yusei, Jack, and Crow Hogan; Devack, who stole the Ancient Fairy Dragon card, Luna's Signer Dragon; Misty Tredwell, a model who blames Akiza for the death of her brother Toby; Greiger, who blamed Rex Goodwin for his village's disappearance; and briefly Carly, a blogger with feelings for Jack. With the help of Leo, Luna's twin brother, and Crow Hogan, Yusei and Jack's best friend, they are able to defeat the Dark Signers. However, Rex Goodwin reveals that he has become a Dark Signer and uses his brother's severed arm to become a Signer, seeking to rebuild the world in his image using the power of both light and shadows. Yusei, Jack, and Crow then face him in a Turbo Duel in order to stop him and the King of the Netherworld from finishing off the Signers and destroying the world. Before the final attack, Yusei gains the Head mark, making him the new leader, while Crow gains his former Tail mark, making him the fifth Signer. With the power of the Crimson Dragon and Yusei's Majestic Star Dragon, he defeats Goodwin, who, along with Roman, sacrifices himself to destroy the King of the Netherworld and revive the Dark Signers as normal people.
After the Dark Signers' defeat, Neo Domino City and Satellite are reunited into one prosperous city with the building of the "Daedalus Bridge", an net of roads linking them with some sections also used for Turbo Duels. Yusei and his friends, now calling themselves "Team 5D's", prepare for the upcoming World Riding Duel Grand Prix (WRGP) 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 fellow competitor Sherry LeBlanc, who is investigating the Iliaster organization due to them being reportedly responsible for her parents' deaths. Team 5D's is also joined by a mysterious amnesiac mechanic named Bruno, who befriends the team and helps them prepare for the WRGP. The WRGP soon begins, with Team 5D's facing tough opponents such as Team Unicorn, a world-ranked dueling team, Team Taiyo, a new dueling team who started with nothing, and Team Ragnarok, who possess special abilities like the Signers. Yusei and Jack develop the "Clear Mind" and "Burning Soul" abilities, respectively, upgrading their ace monsters into forms capable of dodging the Machine Emperors' absorption effects. Team 5D's eventually confront the Emperors, who are revealed to be three different incarnations of Aporia, a cyborg sent from the future to destroy Neo Domino City and 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, threatening to crash into and destroy Neo Domino City, and they climb aboard the Cradle to stop it. Before reaching the core of the fortress, they confront three individuals guarding its access: Akiza 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. Leo dies during the duel and is revived by the Crimson Dragon, becoming the sixth Signer bearing the mark of the dragon's Heart. The Signers finally reach Z-one, Iliaster's leader, and Yusei borrows his friends' dragons to add them to his deck, challenging Z-one to a final Turbo 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. Using his friends' cards, Yusei performs a "Limit Over Accel Synchro" and summons his strongest monster, "Shooting Quasar Dragon", defeating Z-one. Z-one decides to entrust the future of mankind to Yusei before sacrificing himself to destroy the Ark Cradle and save Neo Domino City from destruction.
Several months later, following a final duel between Jack and Yusei, the former members of Team 5D's go their separate ways, with Yusei staying behind in Neo Domino City to research a way to stop the destruction of humanity in the future. As they drive off, the Crimson Dragon appears for the final time and removes the Dragon Marks on the Signer's arms, signifying that the danger has now passed. The Signers leave the city knowing they will be connected with each other and will return after fulfilling their dreams.
