Seasons & episodes

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.

Crow uses his Duel Runner’s modifications to survive Greiger’s attack. Yusei decides to jump into the geoglyph in order to discover who was dueling, and is shocked to find Greiger is a Dark Signer. Yusei tries to calm both of them down, but neither refuse to let up. Crow recalls that he had no friends when his father died, but thanks to finding some Duel Monster cards, he was able to learn how to read and make friends with other duelists, including Yusei and Jack, and soon grew to take care of others in the same way…

Greiger summons his Dark Synchro, which is Dark Flat Top, which allows him to special summon another Flying Fortress SKY FIRE, and then attacks Crow with it, which reduces Crow's life points to down 100. Crow crashes, but remains determined to win, and gets back into the game. Using a pot luck with his trap, he manages to defeat both monsters, but this in turn, allows Greiger to summon his Earthbound Immortal, Chacu Challhua. Crow manages to Synchro Summon Blackwing - Silverwind the Ascendant, and prepares to destroy Chacu Challua with its special ability, but then, he, Yusei, and Greiger notice that the souls used for its Chacu Challhua's summoning were the people of his village, and Greiger's siblings. Realizing it was the Dark Signer's fault, and not Goodwin's, Greiger wants to stop the duel, but the Earthbound Immortal refuses to give up, and takes over his body. As he struggles to regain control, Greiger asks Crow to finish the battle.

Yusei finally catches up with Kalin and start what Kalin calls 'The Last Duel of the Enforcers'. Yusei hopes that this duel will rekindle their friendship. After the Enforcers took over the Satellite, Kalin kept looking for enemies. When those enemies started including young kids, Crow and Jack left the team, leaving just Kalin and Yusei. When Security shows up in Satellite with Duel Runners and Kalin plans on destroying them, Yusei also quits the team. Kalin decides to attack Security, getting their attention by blowing up some confiscated Duel Disks. When Yusei, Jack and Crow catch wind of Kalin's actions, they go to look for him and find him cornered in a building ready to stand off against Security. Back in the present, Kalin summons his One-Hundred Eye Dragon and begins to utilize his Handless combo.

Yusei defeats One-Hundred Eye Dragon, but is fully aware that it allows Kalin to draw his Earthbound Immortal to his hand. Back in the last days of the Enforcers, in a flash-back of Yusei's memories, Yusei, Jack and Crow try to talk sense into Kalin, and they all end up running away from Sector Security. One Sector Security officer pins down Kalin, but he manages to jump on his Duel Runner, causing him to crash with a bad head injury. He tries to finish him off but Yusei stops him. Yusei tries to pose as the leader of the Enforcers in order to protect Kalin, but the chief of Sector Security at that time had already figured it out that Kalin was the real leader of the enforcers, and Kalin becomes furious when he sees his hand on Yusei's shoulder, thinking Yusei had ratted him out. Kalin then gets harsh treatment in prison, losing his deck, and he was eventually convinced by the voice of Roman to become a Dark Signer.

With Kalin and Ccapac Apu defeated, all the Satellite residents are returned. Just then, Roman uses one of his dark spiders to possess Trudge and talk to Yusei, coaxing him to find him at the Original Ener-D Reactor, challenging him to a duel. Lazar is seen talking to a mysterious figure. Goodwin goes to meet with Roman. Roman is shown with a shadow duel disk, and challenges Goodwin to a duel, as part of a promise they made. Yusei, Luna, Leo, and Trudge traverse down the crater, whilst Crow, who notices the army helicopters, takes a different route. Yusei encounters Roman on a bridge, who activates an explosion, causing a flux of Ener-D to appear underneath them. They start to duel and manages to attack Roman with Junk Warrior, although this in turn allows Roman to summon Earthbound Immortal Uru. Roman continues to put pressure on Yusei and manages to bring his life points down to 100.

After bringing Yusei's life points down to 50, Roman begins to tell him of what happened 17 years ago between him, Rex and Yusei's father. They were working on the Original Energy Reactor, but Professor Fudo wanted to stop the project when it started to look unstable. Roman had decided to travel to the Nazca lines, where he encountered a mysterious person, claiming to be from Yliaster, who knows about Roman's birthmark. The mysterious man convinces Roman to look into the light coming from the reactor, where he is struck by dark energy and is shown the history of the Earthbound Immortals and the mighty powerful Crimson Dragon. Meanwhile, Crow finds Rex, who explains that Professor Fudo was betrayed by Roman. He shows off four Dragon cards, but Professor Fudo manages to escape with three of them, but got severely injured in the process and entrusts the cards to Rex.

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.

Akiza and Mina arrive at an abandoned amusement park where Ccarayhua's control unit is, shortly followed by Yusei's group, and a man claiming to be sent by Goodwin. Misty traps Akiza in a Hall of Mirrors, actually dueling her through the mirrors. She uses cards that block off drawing cards from the deck, and also shows Akiza the events involving Misty and her brother, Toby, who apparently met her at Arcadia Movement. Yusei is led to a room where Mina is found unconscious and is attacked by the man who turns out to be Sayer, who had survived his duel with Carly, and is determined to reclaim Akiza. He uses his psychic abilities to knock Yusei in a cage with Mina as it slowly fills with water. Trudge eventually finds them and tries to free them. Akiza is shown the moment where Toby was killed, which led Misty to become depressed and crash her car, transforming her into a Dark Signer.

With Akiza's dormant physic abilities fully awakened, Misty activates her geoglyph. Trudge manages to free Yusei and Mina and Yusei goes to join Luna and Leo. Learning about Akiza's current state, Yusei goes to face Sayer, who reveals he is controlling her mind and was responsible for Toby's death. Misty summons out her Earthbound Immortal Ccarayhua. Sayer talks about the experiments he performed on Toby seeing that he did not have ultimate psychic powers sent him to an unknown location that not even he knows about. However, Yusei revealed he had activated an intercom on his duel disk, letting Misty know what Sayer had told him. Angered, Misty gets Ccarayhua to eat him, freeing Akiza from her trance. Misty apologizes to Akiza, but the Earthbound Immortal forces her to continue dueling. Akiza defeats her, setting her free, which results in her being sent to the netherworld. The New Domino City residents return, but a Dark Signer mark, the mark of the Condor appears in the sky.

As the Condor geoglyph shines in the sky, a massive monster emerges from the Original Ener-D Reactor and heads towards the Condor geoglyph over New Domino City, which was the King of the Netherworld. The Crimson Dragon appears and sends everyone to the front of a temple (the Altar of the Dragon Star), where they find Goodwin, who reveals himself to be a Dark Signer. Then, he transfers Roman's mark of the Dragon Head from a canister to his left arm, destroying the metallic arm that was covering it at the same time. He challenges Yusei, Jack and Crow to a Turbo Duel in the air. Goodwin reveals that he lost the duel with Roman prior to his battle with Yusei on purpose, and became a Dark Signer in order to end the pointless cycle. He summons out both a Synchro monster; Sun Dragon Inti, and its Dark Synchro counterpart; Moon Dragon Quilla. He also reveals he was the Legendary turbo duelist who constructed and flew across the Daedalus Bridge.

After being dealt some direct damage due to the cooperative efforts of Yusei, Jack and Crow, Goodwin is able to summon his Earthbound Immortal - Wiraqocha Rasca, absorbing the souls of New Domino City. Then, the King of the Netherworld spouts forth several beasts that attempt to attack the players. However, they are saved by Black Rose Dragon and Ancient Fairy Dragon. Crow sacrifices himself by playing a trap card in order to protect Yusei from Wiraqocha Rasca's special ability, and falls unconscious. Goodwin coaxes Jack into attacking him, but after he gives in and loses some life points, Goodwin's statement of becoming a dark signer causes Jack to remember what Carly taught him and decides not to do things his old fashioned way anymore. Goodwin laughs at the idea of the bonds of true friendship and love, saying that destiny is all that there is.

Goodwin reduces Jack's life points to 1, and gets the King of the Netherworld to attack him, causing him to crash. Yusei's life points get reduced to 1 too, before he summons his Stardust Dragon and takes advantage of the traps Crow and Jack placed beforehand. As Yusei tries to reach Goodwin, which he successfully does, he regains the Signers' marks from him. Furthermore, Yusei gains Roman's mark of the Dragon Head, and the mark of the Tail that Yusei used to have transfers over to Crow. Yusei then takes the marks of the other 4 Signers, and gains the Seal of the Crimson Dragon. Then, he summons the Majestic Star Dragon and destroys Earthbound Immortal Wiraqocha Rasca, which defeats Goodwin. Then, the Crimson Dragon envelops the Majestic Star Dragon, infusing it with the power of the Crimson Dragon, and dives into the King of the Netherworld.

Six months after the battle between the Dark Signers and the Signers, a large stone tablet falls (which is Machine Emperor Wisel Infinity's tablet) from space and lands on Earth, just outside of New Domino City. Whilst investigating it, Lazar encounters three people from Yliaster, who are Jakob (the leader), Lester (self-appointed sub-leader), and Primo (the lowest-ranking member). Lazar questions them about their intentions, but after being reminded by Primo that they were his leaders, and a brief outburst in which Primo points the tip of his sword at Lazar's neck, he quickly submits to the trio, and turns over the leadership of New Domino City to them. Then, Primo tells the other members of the trio that he was going to take his Machine Emperor out for a "test drive." A day later, Sector Security investigates a turbo duelist named Ghost, who is attacking Turbo Duelists, and "stealing" their Synchro Monsters, at night.

Yusei summons out his Stardust Dragon and deals some damage to Ghost. However, Ghost uses his Machine Emperor Wisel Infinity's special ability to absorb Stardust Dragon, which causes Stardust Dragon's attack points to be added to Wisel's, boosting its attack points from 2,500 to 5,000. Yusei puts up a good defense, but finds himself pressured. After hanging on for a while, Yusei remembers that he has a second chance, and uses Speed World 2's effect the Crimson Dragon's power to draw another card during his draw phase, which grants him the tuner monster Majestic Dragon, and he is able to retrieve Stardust Dragon using the trap card Syncro particle, and summons the Majestic Star Dragon, and then attacks Wisel Top, resulting in the destruction of the rest of the Machine Emperor, defeating The Ghost. The Ghost then crashes into a forest, and one of the 3 emperors of Yliaster, Primo, retrieves Ghost's duel disk, and his own Wisel deck from The Ghost's duel runner.

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.

Yusei, Jack and Crow pay a visit to Martha and Blister, where Blister talks to them about the asteroid crater. Crow is asked to retrieve an old man named Bashford who refuses to leave his house due to family ties. However, the route to his house is filled with booby traps. He ends up on top of an old-fashioned Dueling Arena (which Bashford had built himself, in hopes that his son Koki would return and duel him), (Dueling Arenas were first used, in the first season of Yu-Gi-Oh! Duel Monsters) and challenges Bashford to a duel. He finds himself under pressure from his Bashford's Scrap-Iron deck, but he manages to make a comeback. The effects of the battle causes the duel arena and the house to collapse, but Crow manages to win the duel and help Bashford. Yusei manages to retrieve a family photo from the house before it collapsed. Bashford thanks them and returns to Martha's place.

Families find themselves under pressure from a loan shark named Don Pierro who takes their precious cards. Crow gets angry at Jack for drinking expensive coffee and suggests that he gets a job. However, his ego gets him kicked out of several jobs. He and Carly follow a boy named Marco to a shrine, where he leaves his cards that were deemed unworthy by Pierro. Jack decides to challenge Pierro for everyone's contracts, putting his Red Dragon Archfiend and Duel Runner on the line. Pierro puts pressure on Jack by implementing his Loan Tokens, damaging his life points. However, Jack manages to win using Marco's cards and destroys all of Pierro's loan contracts. However, he still can't get a job.

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.

Yusei wakes up to find himself being carried away inside a truck after being ambushed by someone named Ichiro wanting to recruit him for the Grand Prix. When Jack, Crow, Akiza and Mina hear about his capture, they go to look for him. Akiza manages to locate the truck Yusei is captured in, and is surprised to find no one is driving it. Akiza uses her powers to break it open, but ends up trapped on their with Yusei when the truck speeds up. They escape, but are then challenged to a Turbo Duel by a mysterious rider. She brings out a fusion monster whilst Yusei responds with Junk Warrior, and Akiza finds herself moved from witnessing a Turbo Duel first hand. The rider then brings out her ace monster and reveals herself to be a woman named Sherry Le Blanc, hoping to recruit Yusei to her team.