After his victory over Jack in the Fortune Cup, Yusei is named the new Duel King. While Yanagi informs the gang about the Signers and the Dragon Birthmarks, Yusei is challenged by a mysterious man with a Spider shaped birthmark on his arm who is able to make the duel into a Shadow Duel. Yusei is surprised to find his opponent has a fearsome new type of monster, a Dark Synchro Monster. Meanwhile, a reporter named Carly tries to get the scoop on the new Duel King.

Despite the difficulties caused by the Dark Synchro Monster, Yusei manages to win his duel against the Dark Signer. However, after the duel, his opponent has no recollection of what happened and no longer has the birthmark or any Dark Synchro Monsters in his deck. It is revealed that spiders are being used to control people, one of which are heading to the hospital where Jack is recovering. Trudge arrives to take Yusei back to the Satellite, and Yusei decides to go, with intention of getting the truth out of Goodwin.

Following her release from security, Carly attends a premiere event and encounters a model named Misty, who predicts her death. When Angela, a rival reporter, reveals Jack was actually born in the Satellite, Carly decides to infiltrate the hospital to interview Jack. At that time, a Dark Signer spider possesses Trudge and challenges Jack, who is trying to leave the hospital, to a duel. Unable to use his fractured right arm, Jack decides to use Carly as his arm. They win the duel, but Jack is weakened and asks Carly to get him out of there without anyone noticing. Meanwhile, Goodwin shows Yusei the truth.

A Satellite rebel named Crow steals several decks for his friends. He is forced into a duel by Security, but manages to beat them with a one-turn kill. As Goodwin tells Yusei the truth about Signers and Dark Signers, Luna has nightmares involving the dragons. Mina and Trudge show up at Carly’s place where they find Jack, but he refuses to go with them. Yusei is then sent back to the Satellite where Crow awaits him.

After catching up with each other and reuniting with Rally and co, Yusei and Crow are forced into a Turbo Duel with security using Tag Duel rules. Meanwhile, Carly accompanies Jack around the city whilst Mina and Trudge follow. Jack reminisces about his life in the Satellite, and the friends he betrayed. Following some advice from Carly, he decides to follow his own path.

Rally and friends meet up with Yusei and Crow at his hideout, where Crow tells a story about the man who made the Daedalus Bridge. Later that night, whilst Yusei and Crow search for the Dark Signer’s whereabouts, Kalin, a former friend of theirs, sends out a Dark birthmark signal, alerting Yusei and the other Signers. Jack and Carly are escorted by Mina to Yusei’s whereabouts, where Carly learns that Yusei was born in Tops, and his parents were involved in the Zero Reverse incident. Kalin makes his appearance, trapping Yusei in a geoglyph shaped like the Giant Nazca Line and forcing him into a Dark Turbo Duel.

While preparing for his duel against Kalin, Yusei, Crow and Jack remember when they were all part of a duel gang, the Enforcers, who duelled rival gangs at night. The duel starts and Yusei takes a harsh attack due to the effects of the Shadow duel, which appears to be more dangerous in Turbo Duel.

Kalin summons his One-Hundred Eye Dragon, a Level -8 Dark Synchro monster, causing a real threat to Yusei. Yusei once again recalls his days in the Enforcers, and remembers how Kalin once saved his life. When he is almost burned in the fires of the dark barrier, Yusei also remembers when Kalin killed a member of Security and how the proceeding fight between them sparked Kalin’s hatred towards Yusei.

Yusei defeats One-Hundred Eye Dragon using Stardust Dragon, but Kalin summons a powerful monster, an Earthbound Immortal, called ‘Ccapac Apu’ using the souls of all the captured Satellite inhabitants, unphased by attacks from Monsters, Spells or Traps. Before it can attack, Yusei’s Duel Runner gives out and crashes, ending the duel. However, Yusei is impaled by a shard in his abdomen and is taken to a local doctor in Satellite by Crow. Meanwhile, Yusei’s friends try to retrieve his broken Duel Runner while staving off Satellite thieves. However, in the english adaptation, Yusei suffers internal bruising to his abdomen after his duel with Kalin.

As Yusei recovers from his operation, Leo assumes he is the Fifth Signer since his monster, Power Tool Dragon, apparently appeared in Luna’s dream. He comes up with the idea of recruiting Akiza to fight the Dark Signers and goes with Luna, Tanner and Yanagi to visit Sayer in order to see her. However Sayer gasses them, and has his own plans of recruiting Luna into the Arcadia Movement, locking up Tanner and Yanagi and forcing Leo into a duel with his sister on the line, for if he loses Luna will stay and become a member of the Arcadia Movement, while Luna watches with Akiza. Leo temporarily gains the upper hand by summoning Power Tool Dragon, but is then defeated by Sayer’s Synchro Monster and is left unconscious.

Jack decides to return with Mina to the city to retrieve his Duel Runner. He thinks it is too dangerous for Carly to get involved but promises to tell her everything when it’s all over. Carly, wanting to maintain her contact with Jack, decides to look into Akiza and the Arcadia Movement, and finds out Misty is somehow linked to them and goes to meet her. She reveals that Akiza was apparently responsible for the death of her younger brother.

New Domino City is shaken by an earthquake as a new geoglyph is set ablaze. To Sayer’s surprise, somebody shows in his office: Carly, alive… and as a Dark Signer. She challenges Sayer to a Shadow Duel for revenge, and Sayer is shocked by her new monsters’ abilities. Noticing the geoglyphs, Jack heads towards the action, almost being engulfed by the flames in the process. Meanwhile, Akiza is approached by Misty, who challenges her to a duel, as a dark signer as well.

During their duel, Misty informs Akiza that she is responsible for the death of her brother, which Akiza denies. Tanner and Yanagi rescue Luna and Leo from their imprisonment, and discover the two duelists along the way. A barrier coming from Luna’s birthmark protects the others as countless souls are sacrificed when Misty summons her Earthbound Immortal, Ccarayhua.

Akiza is taken to hospital where her parents, Hideo and Setsuka, meet up with Jack, Leo and Luna. Jack tells them that the only one who can save Akiza is Yusei, so Hideo travels to Satellite to talk with him. He tells him that when Akiza was young, he was unable to spend time with her due to work. When they finally were able to spend some free time together, a call from work interrupted, which frustrated Akiza and awoke her Signer powers and birthmark, hurting her father in the process.

Enduring the pain of Akiza’s attacks, Yusei summons Stardust Dragon to face against Black Rose Dragon and reach her heart. Still hurt by the loss of Sayer, Akiza unleashes her full power and constantly weakens Stardust Dragon. As Yusei gets hit by more attacks, Hideo steps in to protect him and try and reach Akiza, taking some damage in the process.

Before visiting Goodwin, Mina shows Akiza the true nature of the Arcadia Movement, showing how they performed experiments on young children in order to raise Psychic Duelists. Yusei, Jack, Akiza, Luna and Leo go to Goodwin in order to get the truth. Goodwin almost denies Leo entry, since he is not a Signer, but Luna insists that he stay with them.

The Signers contemplate about what Goodwin had told them. Yusei blames himself for Kalin becoming a Dark Signer, but Jack punches him in the stomach and face to knock some sense into him Yusei then punches back. Leo is reluctant to join Luna in going to the Satellite, since his battle with Sayer proved he wasn’t a worthy hero.

Crow manages to regain some ground in his duel against Lazar with his monster, Black Feather Arms Wing, but just then, a purple light shines from the Original Enerdy Reactor within a crater Lazar was investigating, and a black fog starts to envelope Satellite. Whilst Lazar manages to escape, Crow gets caught up in the fog and disappears, along with several Satellite citizens.

While flying to the Satellite Akiza asks about Yusei’s father and Mina explains to everyone what his father did. She also explains what happened 17 years ago and that Yusei is city born. Yusei, Jack, Akiza, Leo, Luna, Mina and Trudge arrive Martha’s house where she and Blister are waiting. Martha informs everyone that Crow, Rally and the others have gone missing, and offers everyone a meal. Then Yusei answer Martha’s question if the girl that’s sitting there at the table is Akiza and then Martha states he saved her.

As Roman prepares for his Earthbound Immortal summoning, Yusei tries his best to postpone it and Martha and Trudge hurry to save the children. However, Roman then speeds up the process and is able to summon his Earthbound Immortal, Uru. Thankfully, Jack arrives on time and forms a barrier around the children to stop their souls being sacrificed. Roman then reveals that not only was he an assistant to Yusei’s father, but is also Goodwin’s brother and the one responsible for the Zero Reverse incident. Yusei manages to deflect an attack from Uru’s attack, but it hits a building Taka, Martha and Trudge were hiding in.

The Dark Signers show up to taunt the Signers following Yusei’s duel with Roman. Devack introduces himself and reveals he is in possession of Ancient Fairy Dragon and challenges Luna to come get it. Roman announces that their duels will take place at the four stars of destiny. Whilst chasing after them, Jack discovers that one of the Dark Signers is Carly, who tells him to find her if he wants to know what happened.

As Luna reaches a town in the Spirit Realm, she notices that its inhabitants are running frightened, and gravity is behaving oddly. She is discovered by a group of monkey soldiers, who imprison her card spirits in stone tablets with minus levels. She is rescued by a young mage named Torunka, who decides to help Luna find Regulus, the servant Ancient Fairy Dragon spoke of.

As Luna and Torunka manage to find Regulus, Luna notices he has a Minus Staff stuck in his leg, causing him to hear the opposite of what Luna says and become distrustful of her. Luna manages to steal one of the foot soldier’s Minus Staffs to negate the one on Regulus, and when he notices she is a Signer, he decides to help them.

Luna’s plan to free Ancient Fairy Dragon is hampered when the Minus Staff she was carrying gets revealed, causing Torunka to accidentally blurt out their plans. Regulus manages to destroy Zeman, who is simultaneously destroyed by Leo in the real world, but not before Zeman transfers the power of the minus curse to Devack. This returns Torunka to his normal age, but doesn’t free Ancient Fairy or the minused spirits.

Leo and Luna defeat Devack, and he disappears, freeing all the trapped spirits. Ancient Fairy Dragon and Regulus give their thanks to Luna, and becomes cards in her deck. Luna places the Ancient Fairy Dragon card in the control unit, deactivating it. Making sure everyone is safe, Yusei decides to head towards Kalin. Hearing about Devack’s defeat, Roman sways Greiger over to his side, and executes him in order to transform him into a Dark Signer.