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.

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.

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.

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.

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.

With Roman's defeat, all the Satellite citizens, including Martha and Rally, are returned. Jack finally meets up with Carly, but she is reluctant to be helped and challenges Jack to a Turbo Duel. Initially, Jack is reluctant to fight and takes a lot of damage, but he starts to fight back, as he does not believe Carly is a person who would hurt people. Carly traps Jack in a vision where he is transformed into a Dark Signer by Carly and becomes destined to destroy the Crimson Dragon by her side. However, noticing Carly's glasses, Jack breaks free of this vision, and decides to fight for what Carly truly desires. Meanwhile, Yusei finds himself in a strange place surrounded by the spirits of those who died in the Zero Reverse incident. Due to Yusei's connection to the incident, they start to attack him, but he is rescued by a strong white light and the voice of a familiar figure.

Jack activates a Trap that lets Carly choose the outcome. He manages to break through to Carly and she makes the right choice. However, the Earthbound Immortal takes over her body, forcing her to continue the duel. Jack brings out his Red Dragon Archfiend in the hopes of freeing her. Meanwhile, the mysterious spirit reveals himself to be Yusei's father, who returns him to the real world. Carly summons out her Earthbound Immortal - Aslla Piscu, but Jack manages to stop its attack. Jack expresses his feeling for Carly, and then he takes the marks of the other Signers, gives him the Seal of the Crimson Dragon. Hearing the real Carly's pleas to end the duel, despite his objections, Jack synchro summons Majestic Red Dragon. Jack hopes to end the duel in a tie, taking him down with her, so that he can still be with her, but Carly activates a trap card so that only she would lose. Jack is able to do nothing but hold Carly tight, as she disappears into the Netherworld.

As Yusei and Crow work on their new engine, they are visited by Leo, Luna and their classmates, including the timid Sly, who is nearly tempted to steal Stardust Dragon. Yusei is asked by the Academy's principal to fix something, which turns out to be the head instructor, Rudolph Heitmann, who is threatening to expel Leo, Luna, and their friends for using low level monsters. Yusei arrives, and challenges Heitmann to a duel, in order to stop them getting expelled, and to prove the strength of low level monsters. Heitmann manages to summon three Ancient Gear Golems on his first turn and deals a lot of damage. Yusei summons out Stardust Dragon, but sacrifices him to summon out several Tuner monsters, which belong to the relevant students. Yusei manages to use them to defeat Heitmann, who learns his lesson, and withdraws the expulsions. As Yusei leaves, Sly contemplates to steal Stardust Dragon. Fortunately, he will never get that chance.

Whilst Leo, Luna and Dexter go wandering through a forest, Luna senses an atmosphere, drifts out of consciousness and follows it, despite warning from Kuribon and Regulus. When she awakens, Luna encounters a boy named Hayley who is looking after a doll representing his sister, Claire. When they notice she has gone missing, Dexter goes to Yusei for help whilst Leo chases after her. When Leo approaches the house, Hayley feels threatened and goes to duel him. Leo notices the damage Hayley is dealing is similar to a Psychic Duelist's, and summons out his Power Tool Dragon. Yusei arrives and busts into the house and finds a load of people trapped inside cards. Meanwhile, Luna is able to talk with the spirit of Claire. Hayley summons out Hollow Ghost and deals some harsh damage to Leo, but Leo manages to turn it around and win the duel. It is revealed that Hayley had died along with his sister, but didn't realize it, which was what kept him there.

Jack and Carly investigate some Duel Runner thefts. While chasing after a group of them, one of the members, who is actually an undercover agent named Kaz, gets injured. Jack feels responsible for causing the accident, and tries to investigate the matter himself, but is ganged up on and knocked out. He doesn't give up, and soon comes across the entire gang again, where he is once again beaten. However, he was able to place a tracker on one of the members, and finds their hideout, which is located on a large ship. The boss, Syd, challenges Jack to a duel in which the loser is thrown into a crusher. Syd gets the upper hand early on, and despite Jack summoning several monsters, he still finds himself countered. It is soon revealed that their hideout is on a tanker, which has sailed out of range from Sector Security.

Sector Security bursts in with a warrant for Jack's arrest. Mina and Trudge show footage of something similar to Jack's Duel Runner causing other people to crash in duels using Red Dragon Archfiend. Yusei and company recall that earlier, Jack had fallen out with them over sticking to his usual plays. Jack still denies committing any crimes, and Crow doesn't help. As a result, Jack is arrested and sent to jail. When news spreads, everyone else has a hard time believing it. Later that night, an electronic bug breaks open Jack's cell, allowing him to escape. However, he then runs into an identical Jack Atlas riding an identical Duel Runner and behaving like Jack in his "Duel King" phase (from Season 1), and is challenged to a Turbo Duel. Jack draws a Tuner Monster that can summon Red Dragon Archfiend, but refuses to use it due to the earlier argument, and summons Exploder Dragon instead. He initially gains the upper hand, but is shocked to find his tactics dubbed weak by the impostor.

Wanting to find out the truth behind Jack's alleged crime spree, Carly meets with a pair of hippies who caught a picture of two of Jack's Duel Runner. She replays this to Yusei and Crow, who search the crash site only to find one of Jack's cards. The real Jack is trapped in a virtual prison of sorts, made by the Yliaster trio, forced to watch his impostor ruin his reputation. Yusei and Crow catch up with the impostor, but are attacked by his thrusters. Hearing his friends kindness, Jack breaks free from his imprisonment, and catches up with his impostor for a rematch. This time Jack learns from his mistakes and uses the right Tuner Monster to summon Red Dragon Archfiend. The impostor then summons his own Red Dragon Archfiend but Jack manages to destroy it. However, the imposter then manages to revive it, and summons two more Red Dragon Archfiend copies. Jack manages to survive his attack and is granted the power to summon Majestic Red Dragon by his Mark of the Dragon.

Yusei manages to survive Andre's onslaught, but still takes a lot of damage to his life points, especially when Andre brings out his Synchro Monster. Yusei summons out Stardust Dragon and destroys his monster, but before Yusei can win using Speed World 2's effects, Team Unicorn's practice time ends, along with the duel. The next day, Sherry briefly visits Yusei to ask about the thing they both saw, and Martha's kids give Crow a banner they made. This inspires him to train, but he suddenly crashes and breaks his arm, leaving him unable to participate, so Akiza offers to take his place. Crow, whilst initially furious at the decision, offers to coach Akiza in her training.

Yusei manages to destroy Andre's key Speed Spell card, but in doing so allows Andre to activate that, despite knocking himself out, takes a huge chunk out of Yusei's life points. Yusei then faces Team Unicorn's next duelist, Breo, who soon summons his Synchro monster, Voltic Bicorn. He soon destroys it however in order to implement his deck destruction tactic.

After Yusei and Bruno mutter about this transformation being Primo's true form, Primo demonstrates to Yusei one of his new abilities. He causes his Machine Emperor to create a field of energy, which causes glass everywhere in New Domino City to shatter, and results in blackouts. Remembering the destruction caused by the original Ener-D reactor spun in reverse, Yusei screams, "Stop," and rams Primo's duel runner. Startled, he loses concentration and the destruction stops. Frustrated, he calls Yusei "inferior." When Yusei demands Primo to ressume the duel, Primo rides up besides Yusei, and then activates his own battle Royale Mode. Yusei begins his duel with Primo by summoning out Junk Destroyer and manages to deal some damage. Primo becomes furious, and gets his Machine Emperor Wisel to create another field of energy, which results in lightning bolts striking everywhere in New Domino City, causing electrical devices to fail.

With Stardust Dragon absorbed by Machine Emperor Wisel Infinity, Yusei becomes frustrated over why his attempt at performing an Accel Synchro didn't work. Barely managing to survive Primo's attacks, Yusei eventually manages to retrieve Stardust Dragon. Primo uses his Machine Emperor to start a tornado to affect the city, also putting a child named Haruka in danger, but Akiza manages to save her without using her psychic powers. Then, Primo has Wisel create another field of energy, this one to torture Yusei, panting, and in pain, the marks of the other Signers reflect the pain that Yusei is feeling. Regaining his determination and clearing his mind, Yusei finally manages to perform an Accel Synchro, and summons Shooting Star Dragon, which flies into the tornado, and disperses it, and then flies up into the sky to shine its light on New Domino City.