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.

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.

The duel between Yusei and Sherry continues, with Akiza insisting that she stay and spectate. Yusei brings out Turbo Warrior and deals some damage, and eventually destroys her monster. However, it leaves him in a point where Sherry can win if she draws a Speed Spell, using Speed World 2's effects. Sherry then tells Yusei that she's entering the WRGP to avenge her parents who were killed by Yliaster. Just as Yusei is about to summon Stardust Dragon, Ichiro appears and tries to drop a truck on them. Akiza uses her powers to materialize Stardust Dragon and stop the truck, and Sherry's guardian, Elsworth, beats up Ichiro and his gang. Due to damage to the Duel Lanes, the duel is called off, but they promise to duel again. Akiza is left with a newfound respect for Turbo Duels.

Yusei has a nightmare about Stardust Dragon being captured by The Ghost, and of Sherry's offer. Wanting to learn to duel without relying on Synchro monsters, Yusei asks Jack to duel him. As they duel, they are being watched by a mysterious character (who is really Vizor). Sensing fear in Yusei after being attacked by Red Dragon Archfiend, Jack cancels the duel, saying that there's no way to win without Synchros (Vizor left by the time the duel was over). Later, everyone attends a premiere event for the WRGP, where the details for the tournament are shown. Lazar meets up with the group from Yliaster, who are using the tournament for their own gain. Just then, the party is crashed by a violent Turbo Duelist named Dobocle. Akiza stops him from wrecking the party, and the Yliaster trio become interested in her powers. Dobocle tries to escape, but is attacked by another Ghost, who is really Primo, because he got sick of Dobocle's actions.

Wanting to understand what Turbo Duelists feel, Akiza decides to apply for a Turbo Duel License. Despite initially making lots of mistakes, her determination, along with Yusei's tutelage, allows her to pass the initial exams. Yusei also takes her rollerskating to help her learn how to ride backwards. Yusei then builds her a proper Duel Runner, with the help of Jack and Crow. To obtain her license, she has to beat Trudge in a qualification duel, though she initially has trouble getting to grip with Speed Spells, and her Black Rose Dragon gets beaten. However, she manages to turn it around and summon her Splendid Rose. Some guys, who were furious about losing to Akiza in the initial exams, activate a trap to trip Akiza up. However, using the skills Yusei taught her, she evades the trap and defeats Trudge. With her license earned, Yusei welcomes Akiza to the world of Turbo Dueling. Meanwhile Jack beats up the guys that activated the trap and calls Akiza his friend.

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.

As Yusei and Akiza have a practice Turbo Duel, Leo ponders how he'd fare as a Turbo Duelist. Meanwhile, the Yliaster trio discuss their plans involving the Crimson Dragon, and another tablet crashes into the earth. Later at Duel Academy, a boy named Lester (one of the Yliaster emperors in disguise) enrolls into the school hoping to find out more about Luna, who soon falls in love with Lester. Leo gets annoyed with him asking her so many questions, so Lester uses an illusion to separate him from Luna, and takes her to his mansion. When Leo realizes he's been tricked, he sneaks into the mansion, where Lester shows off an Ener-D powered skateboard that can be used for Turbo Dueling, called a Duel Board, which he gives to Luna. Feeling jealous, Leo begs Yusei to build him his own Duel Board, and spends several days practicing. Luna later joins him in practicing, but they are attacked by another Duel Skater (who is really Lester back in his original dueling outfit) who traps her in a duel.

Realizing Luna and Leo are in trouble, Yusei, Jack, Crow, and Akiza head off to find them. Luna summons out Ancient Fairy Dragon, but it is soon absorbed by Machine Emperor Skiel Infinity. As Yusei and company can only watch, Leo recognizes his opponent as Lester, but Lester states the recognition of his identity has already come to late for them to do anything about it. Luna soon takes some damage in order to protect Leo from Skiel's attacks. Leo summons out Power Tool Dragon, and using traps and monster effects, manages to retrieve Ancient Fairy Dragon. Lester upgrades Skiel and defeats Leo, knocking him off the bridge, but the Crimson Dragon appears and saves him. Luna's counterattack fails, but her Duel Monster spirits prevent her from being hurt, after she loses. When the group try to investigate Lester, they find his mansion gone, and that no one at Duel Academy remembers him. Spurred on by this attack, Yusei becomes determined to learn the Accel Synchro.

Trudge and Mina invite Yusei, Jack and Crow for a fancy dinner, albeit with a motive. They want them to look after Bruno, an amnesiac who recently washed up onto New Domino City. Whilst they initially refuse, they soon discover he is an extremely talented mechanic. Yusei becomes particularly interested in him, as he could help build the engine he needs to perfect Accel Synchro. However, as he spends more time with him, his friends start to get a bit jealous. Yusei and Bruno manage to complete the program needed for his new engine, but it is stolen overnight. Finding a fingerprint on a cup ramen packet, they decide to hack into the Security network to find the culprit, having to complete a puzzle duel in order to gain access. Jack and Crow have trouble going up against Mirror Force, but Bruno uses his intuition to figure out the correct solution. They discover that the matching fingerprint belongs to Lazar.

Yusei, Jack, Crow and Bruno decide to trail Lazar, who had stolen their program for Primo. Noticing he is being followed, Lazar heads to the mall where Yusei and company manage to apprehend him, but he makes a break for it. Lazar manages to lose Jack and Crow using holograms, though Bruno manages to figure out, and he and Yusei follow Lazar to a complex. Lazar gives the program to Primo, who then notices they are being followed and sets off the alarm, separating Yusei and Bruno. Primo activates a dueling Guard Robot filled with Yusei's battle data in order to stall Yusei whilst he installs the program into hundreds of Duel-Bots, collectively called the Diablo. Bruno almost stumbles upon this until he is knocked out by Primo and thrown out of the secret factory when he triggers a lost memory. Meanwhile the Guard Robot uses its high prediction capabilities to block off Yusei's high level monsters and special summons, putting him in a tough spot.

Jack and Crow arrive at the complex only to find themselves locked out, so they sneak in via a ventilation shaft. As Yusei continues to struggle against the Guard Robot, Primo completes their program's installation into the Ghosts, although one of the other emperors of Yliaster, Jakob (the leader), is curious and suspicious of his actions. With his objective complete, Primo starts a self-destruct countdown and leaves using his power, giving Yusei just 10 minutes to win his duel and escape. Jack and Crow join up with Bruno who, reluctantly, have to escape ahead of Yusei. As time is about to run out, Yusei manages to use his monster's abilities to block off the Guard Robot's Lock Deck and summon Stardust Dragon to win the duel. As the complex explodes, Lazar uses his tricks to save Yusei and warns him not to delve any further into the matter.

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's landlord, Zora, is depressed because the city wants to replace the broken cuckoo clock on her clock repair shop. Later, the gang are visited by Zora's son, Lynden, who has returned after three years of training to fix the clock. When he goes to see Zora again, she is not happy to see him, since he was the one who broke the clock in the first place. Before he can run off, Crow challenges him to a duel, forcing him to apologize if he won. Crow runs into a bit of trouble with Lynden absorbing one of his monsters and summoning out his Clock Knight monsters that rely on coin tosses, but soon comes back with his Blackwing Armor Master. Lynden tries to back off from the duel, but Crow tells him he needs to stop running away from his problems. Lynden summons a Time Wizard he got from his late father to destroy Crow's monster. Crow decides to take the damage instead of activating his Mirror Force, since Lynden had realized he can't keep running away regardless of his victory.

Yusei arrives in a desert town called Crash Town, after receiving a letter from a woman named Barbara that Kalin was in trouble. She explains that in this town, there are battles at sunset between the Malcolm family and the Radley group. Yusei is surprised to find Kalin siding with Radley's group, and notices a change in his personality. Kalin uses his Handless Combo and quickly defeats Malcolm's challenger, who is taken away to become a slave in the mountains. Yusei tries to reach Kalin, but he doesn't answer him. Barbara tells Yusei the only way to save him is to beat him in a duel to separate him from the Radley family. Yusei decides to join up with the Malcolm family, earning his place by defeating three of Malcolm's men in one turn, with his Nitro Warrior.

Yusei knocks out Kalin, so they can escape, stumbling upon a graveyard of lost duelists. They then encounter Nico and West who have Yusei's Duel Runner, and learn that their father is still inside the mines. Lawton then finds them, so while Kalin and the kids look for their father, Yusei distracts him with a Turbo Duel. Lawton immediately summons Gatling Ogre, but Yusei's manages to delay its One Turn Kill ability. However, Lawton soon replaces it with Full Armor Ogre. Meanwhile, Kalin and the kids escape on a mine cart and arrive in a different mine. They become surrounded, but Kalin fights them off as West and Nico find their father, setting off to escape again. Yusei manages to beat Full Armor Ogre, but Lawton manages to resummon Gatling Ogre, putting Yusei in a position where one card could mean his defeat.

As Kalin escapes with the kids and their father, Sergio, the pursuers start activating the father's shock collar, but Kalin manages to stop it though nearly falls off the kart in the process. Yusei manages to avoid losing to effects, but Lawton instead summons a more powerful monster. Kalin's group are directed towards a deadly gap, so West and Nico's father jumps to change the tracks to safety, and Sergio falls into the abyss in the process (and dies). Yusei manages to summon Drill Warrior from his graveyard, and Kalin knocks into Lawton before he can respond to it. Lawton then throws some dynamite which sends everyone flying, with Yusei and Kalin falling into a canyon. Lawton kidnaps Nico and West, and along with Barbara overthrows Malcolm. As Yusei and Kalin visit the father's (Sergio) grave, his duel disk reacts to Kalin, who decides to fight with Yusei.

Barbara starts forcing members of the Malcolm family to duel each other to provide new workers for the mines. Yusei and Kalin arrive and challenge Lawton to a duel for Nico and West's freedom and to liberate the town. Lawton gets a handicap to start with 10 cards, giving him easy access to Gatling Ogre's ability. Kalin stops Yusei from negating Galting Ogre's effect and gets attacked. However, he has a special monster, Infernity Zero, whose ability allows him to remain in the duel even with 0 life points, though he will lose if he gains 3 Doom Counters. Lawton manages to destroy the card Yusei used to negate Gatling Ogre's effect in their last duel, but both he and Kalin manage to defend against Lawton's attacks, and Kalin manages to bring up his defense.

Yusei summons his Nitro Warrior and beats Gatling Ogre, dealing some damage to Lawton. However, Lawton summons out Long Barrel Ogre, and Kalin gains another Doom Counter, but Yusei sacrifices his Nitro Warrior to keep Kalin in the game. Kalin and Yusei both summon out their Infernity Doom Dragon ,and Stardust Dragon, but their attacks don't get through. Barbara threatens to harm Nico and West if Yusei and Kalin don't surrender, but the Malcolm family stand up against her. Lawton tries shooting his Shock Gun at Kalin, but is stopped by the arrival of Crow and Jack, who had brought along Sector Security to free all of the miners. Lawton sets off some explosions to escape, but Kalin catches up to him to finish the duel. Lawton makes an assumption about Kalin's cards, but he is defeated, thanks to the effects of Kalin's monsters. Lawton and Barbara are arrested by Sector Security, Crash Town is rebuilt as Satisfaction Town, and Kalin stays behind to look after Nico and West.

Sherry tries to get answers concerning the card her parents were killed over (which is the Z-ONE spell card). She decides the best way to figure it out is to use the Public Security Maintenance Bureau's super computer. The next day, Sherry and Elsworth set off a dummy bomb at HQ, causing everyone to evacuate. When they lock the building down, Yusei and Bruno are left inside, and they soon discover the two. As Bruno follows after Sherry, Elsworth blocks Yusei off, and challenges him to a duel. Elsworth summons his Driven Daredevil, which does great damage to Yusei during his counterattack. Sherry reaches the main computer, hoping to find out the meaning behind her card, but starts fighting Bruno when he shows up. Just then, Bruno's eyes start glowing red and he overpowers Sherry. Noticing her card, he stops attacking and helps her to analyze it. Yusei summons Stardust Dragon and beats Elsworth with a counter trap, and the two catch up to Sherry and Bruno.

Crow goes to visit the grave of Robert Pearson, the original owner of Crow's Blackwing Deck and the Blackbird (Crow's duel runner), who died in an unusual purple fire three years ago. Later, Bruno finds a sealed compartment in Crow's Blackbird that he can't access, which is preventing him from giving Crow's duel runner some upgrades. Crow is later approached by Trudge and Mina, who believe Pearson's death was caused by a duelist using a card called, Crimson Mephist, that dealt real damage, and sent people to the Netherworld. Crow goes to see another of his old friends, Bolton, to ask about the accident. Bolton agrees to talk, but only if Crow duels him, wanting the Black-Winged Dragon card he needs for a loan should he win, even though Crow doesn't know where it is. Crow tells Yusei about how he met Pearson after leaving the Enforcers. The next day, Crow and Bolton start their duel, and Crow has trouble fighting against Bolton's Anti-Blackwing deck.

As Crow continues his duel against Bolton, he makes a small comeback with his Blackwing Arms Wing. However, Bolton then summons out Crimson Mephist, revealing he was the one who killed Pearson. Pearson had refused to sell his Duel Runner rights for a large sum of cash, so Bolton took matters into his own hands. Crimson Mephist destroys Arms Wing and deals some real damage to Crow. As Crow wonders if he can win, he receives encouragement from the kids he's looked after. Crow's mark glows, which automatically keys in the password to unlocking the sealed compartment in Crow's Blackbird. And Black-Winged Dragon, which was hidden inside the compartment all along, reveals itself. Crow then summons it, and uses its special ability to defeat Bolton, who feels remorse for what he had done, and promises that he will change.

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.

The WRGP Preliminaries begin with Team 5D's facing against Team Unicorn. Jack goes up first in the hopes of putting his Power Deck against Andre, who uses an overboost system to turn the corner first, and take the first turn. Jack summons out Red Dragon Archfiend, but takes a lot of damage thanks to Andre's strategy. Andre than summons out Thunder Unicorn, which puts Jack in a tighter spot. Bruno notices a problem in Jack's Duel Runner, but Jack refuses to take a pit stop, and manages to destroy Thunder Unicorn. Yusei realizes that they had been tricked by Team Unicorn into using a Power Deck, but it is too late, as Andre defeats Jack using Speed World 2's effects, the force of which causes his Duel Runner to crash.

Despite his injuries, Jack gets up to push his Duel Runner to the end of the lap to pass the baton over to Akiza, managing to do so before they are knocked out. Akiza immediately summons out Phoenixian Cluster Amaryllis to deal some damage to Andre. However during the next turn, Andre manages to remove it and bring back his Thunder Unicorn. The next turn, Akiza summons out Black Rose Dragon and, to everyone's surprise, Stardust Dragon, which Yusei had given her. However, Andre ends the battle phase before Stardust can attack and uses Thunder Unicorn to beat it. Before Andre can use Speed World 2's effect, Akiza wipes out her own life points to revive Stardust Dragon, in order to pass it on to Yusei. As Yusei continues the fight, Akiza laments that she couldn't help much, but finds encouragement from her parents and the crowd.

Yusei survives Jean's attack and summons Stardust Dragon. He has trouble going up against Jean's strategy, but then Jack stumbles from his bed to give Yusei and the team morale. Yusei Fusion Summons Dragon Knight Draco-Equiste, a move Jean wasn't expecting, and the two continue to fight through the last of Yusei's deck. Jean manages to survive the strategy laid out by Yusei, and is in a position where he can just end the turn to win due to Yusei's deck not having any cards. However, the duel has given him a desire to fight, and after encouragement from Andre and Breo, Jean launches an attack, which ultimately backfires against him, after Yusei increases the defense points of Rapid Warrior, causing Jean to lose all of his life points, and ultimately, the duel.

Jean give thanks to Yusei for the "fun duel," and the two teams promise to reach the WRGP finals together. As Team 5D's celebrates their victory in their garage, they are visited by Sherry, who had beaten three duelists by herself in her round. They discuss things about Yliaster, and how recent events have been related to them. Sherry reveals they are being targeted by Yliaster, due to them being Signers (not including Sherry). She also talks about the strange experience that she, Yusei, and Bruno had experienced back at Sector Security. After Sherry leaves, Bruno feels weird, and goes to the beach where he washed up upon. Upon finding a cat, it triggers his memory, and his eyes glow red again. The next day, as Yusei and Crow go to watch Team Unicorn's battle against Team Catastrophe, they arrive to find Team Unicorn's Duel Runners crashed, and Andre and Jean hospitalized.

Team 5D's prepare to face up against Team Catastrophe, the leader of which, Nicholas, has been given a Card of Darkness by Primo. Team 5D's are later visited by Breo, and study the memory chips of Jean and Andre's Duel Runners, revealing something had caused their wheels to suddenly lock up and crash, the same reason why Crow crashed. After studying a video Carly gave them, the Signers believe it to be linked to a monster called Hidden Knight Hook. Akiza gets hit by the same phenomenon, and her psychic powers fail, as she loses it, to save her from getting injured. (And, Akiza's psychic powers don't return until Episode 140, after the Ark Cradle appears.) Despite his arm not being fully healed, Crow decides to take her place in their match against Team Catastrophe. The first round sees Crow against Hermann, who instantly summons Hidden Knight Hook. As it uses its effect against Crow's attack, Crow notices a strange hook aim for his wheel and barely manages to avoid it.

Crow continues to bear the pain of his arm, whilst he avoids Hidden Knight Hook's assaults on his Duel Runner. He eventually manages to destroy it, and knock Hermann out by summoning out his Black-Winged Dragon, but when Hermann tries to revive his Hidden Knight Hook, Crow sacrifices his dragon in order to completely destroy Hidden Knight Hook before it can attack him, and then defeats Hermann. His arm at the peak of his pain, Crow passes the duel on to Jack, who begins the next round against Nicholas. Nicholas uses another Card of Darkness, a trap intended to knock both of them out, however it hurts both of them, as Primo has no more use for Nicholas, and allowed his protection against the Card of Darkness to expire. Jack escapes defeat, thanks to his monster's special ability, and rescues Nicholas before he crashes. With Nicholas' Duel Runner destroyed, Team 5D's automatically qualifies for the quarterfinals.

Sherry tries to get the Card of Darkness off of Nicholas, but its card face disappears as soon as she touches it. Meanwhile, the Ghosts start attacking other duelists, overwhelming them with Battle Royale Mode, which makes the battle damage of a duel real. Yusei, Jack, Sherry, Elsworth and Kaz go to help what duelists they can. Aggravated and tired of constantly having his own plans thwarted, Primo orders the Ghosts to gang up on Yusei, who is joined by Sherry and Elsworth. Although they gain the upper hand with their Synchro Monsters, they are soon overwhelmed by the enormous number of Ghosts, and Sherry and Elsworth are taken out, leaving only Yusei to stop them.

Noticing Yusei is in trouble, Bruno, having regained his memories, remembers his mission to protect Yusei and to stop the Yliaster trio at all costs, after being reminded by Z-ONE, transforms into Vizor, calls over his duel runner, and helps Yusei evade the Ghosts. Primo becomes agitated and joins the duel himself. Bruno teaches Yusei about Accel Synchro, about how Ener-D powers through people's hearts and the Clear Mind that can control it. Taking these things into account, Yusei accelerates to top speed and is able to see a new monster. Bruno, who had lost his memory after previously battling Primo, stays behind to duel him again. Meanwhile, Yusei arrives at a crater, where another stone tablet has landed. Upon touching it, he is transported to the white room he had went to before, and receives an Accel Synchro card.

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.

Noticing the light caused by Shooting Star Dragon, Jack and Crow decide to heads towards Yusei. Yusei uses Shooting Star Dragon's special ability, which allows him to once-per turn, draw the top 5 cards of his deck, and Shooting Star Dragon can attack the number of times equal to the number of tuner monster cards drawn. Yusei then takes the marks of the Signers, which allows him to draw 5 tuner monster cards, one per mark (including his own). Yusei then gains the Seal of the Crimson Dragon, with the result of Yusei's lucky draws shocking Primo. When Yusei attacks, Primo manages to block the first 2 attacks by sacrificing Wisel Guard, but the remaining 3 attacks causes him to lose. Primo is unable to believe it, and questions if he was being done in by a human. Then, the rest of Machine Emperor Wisel collapse onto Primo and explode, causing Primo to scream as he loses the rest of his life points.

Greiger has a vision of Jack being destroyed by his own power, so calls both him and Yusei over to the Nazca plains. He talks about how he had built a temple to help seal off the Earthbound Immortals, but lately has been troubled by the appearance of what's known as the Crimson Devil. Greiger warns Jack that using his general power tactics will destroy him, but Jack insists he can only fight using power. Greiger suggests a turbo duel, but Jack is surprised to find his opponent is his little brother, Max, who appears to be possessed by something. Jack summons out Red Dragon Archfiend but finds himself having trouble against Max's special deck. When Jack attacks, he finds himself attacked by his own power just like Greiger's dream, and the duel is called off. Jack becomes defiant about abandoning his power tactic and drives off.

Jack arrives at an abandoned village where he encounters a strange Familiar who reveals himself to be the Crimson Devil's servant, who offers him a chance to gain great power. Meanwhile, Greiger comes to a conclusion that the actions of him and Max were those of the Crimson Devil. Jack, seemingly in a trance, goes into a temple that Greiger had built, leading him to where the Familiar challenges him to a duel. Yusei and company try to follow but are stopped from interfering by the Familiar, who reveals that if Jack loses, his body will become a host to the Crimson Devil, and cuts them off from Jack by creating a very narrow platform, and seals off the only exit. The Familiar announces that he, Greiger, and Max will all become sacrifices to the Crimson Devil. Jack struggles against the Familiar's Yomi deck, which punishes power play.

Jack summons out Red Dragon Archfiend, but is still hampered by the Familiar's Yomi deck, though eventually manages to deal some damage. The familiar tries to use the Crimson Devil's power to knock Jack off his platform, but he hangs in there. Greiger is reminded of a legendary Signer called Burning Soul who once defeated Scar Red Nova alongside the Crimson Dragon, believing Jack to be his descendant. Jack starts to play more strategically and deals more damage to the Familiar. The Familiar becomes angry and summons a powerful monster, bringing the release of Scar Red Nova closer. Just then, Jack produces a Burning Soul and, with the help of the Crimson Dragon, also known as Quetzalcoatl, seals the Crimson Devil forever into the card of Scar-Red Nova Dragon, and performs a 'Double Tuning' to summon that monster and defeat the Familiar, who was later killed by a collapsing wall during the destruction of the temple, due to the power of Scar-Red Nova Dragon's "Burning Soul" attack.

Yusei and the others catch Lazar in disguise stealing some instant noodles. Wanting to find out more about Yliaster, they corner him, but he manages to escape. Hoping to lure him out, the gang hold a fake noodle product launch where people duel Crow in a mascot outfit for a chance to win some noodles. Lazar eventually shows up in another disguise, and whilst they fail to trap him, they manage to put a tracer on him and track him down. Crow challenges him to a duel to get information about Yliaster out of him. Lazar brings out his Jester Lord and seals Crow's tuner monster abilities, but Crow manages to make a comeback and destroy it. As Lazar's family show up to spectate, Lazar makes a comeback with his Jester Queen. Crow holds back his attack out of consideration for Lazar's family, leaving him with the choice of how to end it. Lazar decides to lose and tell the others about Yliaster.

The (Signers) gang, along with Sherry, interrogate Lazar about Yliaster. After some mistarts, involving him just talking about his family and love of cup ramen, Lazar eventually leads them to an arcade game where a puzzle duel is required to be cleared in order to access a hidden database. With three chances, Lazar fails the first time as he does not deal enough damage to win. Akiza uses her knowledge of Turbo Duels to win instead. However, Jack makes a miscalculation in the second round and loses the second credit, leaving Yusei to clear the round himself. With the game cleared, Lazar accesses the data, which reveals the company who sent the three Yliaster members to the Public Information Security Bureau, The Ener-D Express Development Agency.

Yusei, Sherry and Bruno infiltrate the Ener-D Express Headquarters, disguised as representatives of Bolger's company. There, they are shown a new Infinity shaped Ener-D reactor by Clark Smith, which is supposedly designed to allow Turbo duelists to travel through wormholes. Wanting to learn more, they sneak into Clark's office to obtain an access key for Level 10 clearance. When Clark returns, Yusei holds him off by challenging him to a duel with some new rules Clark throws in whilst Sherry and Bruno head for the restricted area. Clark's duel requires players to declare the type of card they want and successfully pick the right one in order to use it. However, Clark gains an advantage by cheating using his glasses. Realizing this, Yusei manages to summon Stardust Dragon and defeats him. However, Clark had already figured out their identities and sets off the alarm.

Clark reveals that he killed Sherry's parents for discovering the secret behind Infinity, which was being used by Yliaster to change history. He sends Yusei, Sherry and Bruno into a wormhole, in which they are doomed to break up and crash. Sherry uses her card to regain control of the shuttle, but ends up getting sucked out. Yusei and Bruno enter a "warped" dimension in the future, and pass by a strange island (a gigantic, floating, upside-down "metallic fortress", the Ark Cradle), where Yusei is briefly visited again by his father, who warns him of an Ener-D that will destroy mankind, before returning him and Bruno to their homeworld (the Present). Unhappy with Clark's actions, Yliaster erases Clark from existence, which spreads a blast of white light across New Domino City. Another WRGP team, Team Ragnarok, also notices the blast, but were protected by their Nordic God cards. Yusei and Bruno regroup with the other Signers, who were defended from the blast by their Signer marks.

After reading up on Team Ragnarok, Leo runs into another WRGP team, Team Taiyo, and injures his knee. After taking Leo to fix up his knee, they tell him about their precious Duel Runner, which got banged up in the Ghost incident, though one of the members, Jinbei, shows disdain for offers of help. Leo gets Yusei and Bruno to help them fix it, and despite Jinbei's objections, the others allow them to help. Meanwhile, Jack, Crow and Akiza attend an exhibition duel featuring Team Ragnarok, with one of their members, Dragan, challenging Jack to a duel. Jack summons out Red Dragon Archfiend, whilst Dragan brings out his Aesir, Thor. As Thor attacks, the powers of both monsters starts to resonate, and causes a quake, forcing Lazar to end the duel before damage can be done. After Yusei finishes fixing Team Taiyo's Duel Runner, he and the others learn they will be facing them in the quarterfinals.

As Team 5D's prepares to go against Team Taiyo, they grow curious from having seen their deck, which consists of mostly normal cards. Taro recalls how he managed to get his team together and enter into the WRGP. The first round starts with Jack going against Yoshizo. Yoshizo brings out Holding Hands Majin to solidify his defense, even managing to defend against Red Dragon Archfiend. It soon becomes apparent that Taiyo's plan is to provide an invincible defense whilst attacking with Speed World 2's effects. Jack manages to equalize their life points, and soon manages to negate Holding Hands Majin's effect and destroy it, however, Team Taiyo have another plan waiting.

Jack beats Yoshizo by countering against Speed World 2's effects, and now faces against Team Taiyo's second member, Junbei, who summons another Holdin Hands Majin. Junbei remembers when he got mad and ran away from home, encountering a man named Mizuru in a sports car. Whilst accompanying him, Mizuru knocks a thug member's duel runner and is chased. When some of Mizuru's friends get captured and Mizuru is too scared to go back, Junbei goes back to face the thugs, and is rescued by Taro and Yoshizo. Back in the present, Jack tries a trick to knock both him and Junbei out, but Junbei manages to survive the attack. Crow continues the battle, who uses the combined efforts of Blackwing Armor Master and Black-Winged Dragon to defeat Junbei. As Taro enters the duel, Yusei suspects that Taro has a plan that will cause them to lose within a few turns.

Yusei manages to deal some damage to Taro, by taking advantage of Stardust Dragon's Defense Mode. As Taro begins his counter attack, Yusei Accel Synchro Summons Shooting Star Dragon. However, Taro activates his own trap, which puts Yusei under the safety line for Speed World 2's effects. Yusei uses the cards leftover from Jack and Crow to negate Zushin's effects, and defeat Taro. Despite their loss, Team Taiyo are praised by the crowd for their efforts. After the defeat of Taro, another part of the Infinity Circuit lights up, and the 3 Emperors of Yliaster gloat about winning the WRGP, and finally setting their plan in motion. Then, the Ark Cradle appears in the sky.

Noticing the appearance of the Ark Cradle (also known as the "Divine Temple") in the sky, Yusei, Jack and Crow go over to investigate, where they run into Team Ragnarok's members, Halldor, Broder and Dragan, who all possess a Rune Eye, similar to the Crimson Dragon marks. Halldor tells them about he got his Rune Eye and his Aesir, later recruiting Dragan and Broder, and uniting them with their powers. Dragan explains that three years ago, his father got hospitalized following a cave in. In order to pay for his hospital bills, Dragan had to follow Goodwin's orders and throw a match against Jack, along with his pride as a duelist. With both sides desiring to fight against Yliaster, the two teams decide to settle things in the semifinals.

Yusei faces not only all three Aesirs, but also a countdown from Halldor's trap card, Gjallarhorn, of which the end of the countdown means that the opponent takes damage equal to the combined attack points of all 3 Aesirs, at the cost of removing from play all 3 Aesirs in order to activate the effect, once the countdown has reached its end. At the End Phase of each of Halldor's turns, Gjallarhorn will gain 1 counter, and once it has 3 counters, its effects will activate. Which means that Yusei has only 3 turns to defeat Halldor. Yusei also had to face Halldor's increasing defense. However, Yusei summons out Shooting Star Dragon and deals some damage, before using the trap, Zero Force, to reduce all 3 Aesirs' attack points to 0, resulting in Yusei taking 0 points of damage when the countdown reached its end. Now that all 3 of the Nordic God Cards have been removed from play, Yusei then has Shooting Star Dragon attack Halldor directly, allowing Yusei to win.

Team 5D's have finally beaten Team Ragnarok after an exhausting battle. With this result, the World Racing Grand Prix (WRGP)'s finals will be Team 5D's Vs. Team New World (the 3 emperors of Yliaster). With the finals looming, Carly ponders the possible outcomes of the upcoming battle, while she writes up her special feature article about Team 5D's. While performing the interview, Akiza and company accidentally reconfirm their bonds. Noticing Carly's struggle to write up an article about Team 5D's, not helped by Mina's interference, Akiza, Luna and Leo decide to help her write profiles for each member, recalling on their past adventures. In addition, when Carly talks to Akiza, they discuss the relation of their new opponents, Team New World, to the organization of Yliaster, and the trio's schemes, causing Carly to gain unthinkable information. When Carly was finished typing all of the information down, Stephanie comes in with a teapot full of hot coffee.

In another dimension, Z-ONE (who has now returned to his original form) shows Sherry a vision of the future, where everything on Earth is destroyed because of a global Ener-D explosion. Then, Z-ONE brings Sherry into the Ark Cradle, which is already emerging into the Yu-Gi-Oh! dimension. That night, the Signers are messaged by the 3 emperors of Yliaster, who tell them about the floating metallic island, the Ark Cradle, where a God called Yliadus (Z-ONE's real name) supposedly sleeps, stating that if they win the WRGP, then Yliadus will awaken and have New Domino City destroyed, but will rebuild it the way the trio wants it to be, which is without the existence of Ener-D and Synchro Monsters. During the next morning, the WRGP finals begin with Jack facing off against Lester, who both bring out their ace monsters, Red Nova Dragon and Machine Emperor Skiel Infinity.

The next round starts with Jack facing Primo, who immediately brings out Machine Emperor Wisel Infinity. Primo then manages to bring Jack's life points down to 1,100, through the use of his trap cards, one of which Lester had intended only for Jakob to use. Seeing that Primo was acting on his own again, when Primo activates 2 traps he left for Jakob, Lester get agitated, but when Jakob reminded Primo of their plan, Primo decided to try something different. Yusei realizes their tactic is based on the continuous trap that Lester left behind, but when Jack tries to destroy it, Primo protects it with a trap card, and gets beaten by Jack. But before he loses, Primo then activates another of Lester's continuous traps, Infinite Prison. By sending Wisel Attack 3 to the Graveyard, he can then treat Wise Core as a spell card from the Graveyard, and set it face-down in the face-down zone.

Yusei begins his battle against Jakob, using Crow's trap to bring out Stardust Dragon when Black-Winged Dragon gets destroyed. Jakob then activates a trap, which brings out Grannel Attack 3, while reducing Yusei's life points to 2,800. Jakob shows Yusei and the others a twisted future where New Domino City is completely destroyed. Due to Synchro Monsters and Ener-D evolving the world at an incredible rate, a war broke out and the Ener-D reactor eventually exploded, destroying most of the world. The Yliaster trio also unveil their memmories of despair. In the future, they see everybody Synchro Summoning, and as a result of them using Synchro Monsters to achieve their own greedy desires, the Machine Emperors show up one day, and begin killing humans. In the vision, as Lester was running with his parents to safety, a Grannel shot his parents down. Lester in the vision, then wails at the death of his parents, the ones who loved him.

After introducing himself, the Yliaster trio's duel runners combine to form Aporia's duel runner. Aporia then combines with it in such a way, that the audience are shocked to the point that they begin wondering if he was human at all. Aporia then activates the continuous trap card, Infinite Prison, so that by sending the trap, Infinity Force from his hand to the Graveyard, he can treat Grand Core as a spell card from the graveyard, and then set it face-down in the face-down zone. He then destroys Infinite Prison in order to add Sky Core, Wise Core, and Grand Core to his hand, which had been set face-down. Next, Aporia sends the 3 Machine Emperor Cores to the graveyard, in order to activate the trap card: Genesis of the Machine Emperors, which allows him to special summons his ace monster, Machine Divine Emperor Mechanicle Infinity Cubic. Then, he causes his Machine Divine Emperor to shoot energy into the sky, which results in lightning striking all over New Domino City.

As Yusei continues to defend himself against Aporia's attacks, Jack and Crow come to join him, despite their injuries. They then provide the traps that Yusei needs in order to reflect Mechanicle's attack. But when Aporia negates Mechanicle's destruction, his life points are reduced from 3,900 to 3,400. Yusei then Special Summons Scar-Red Nova Dragon and Black-Winged Dragon, in order to give Shooting Star Dragon attack points up to 9,600. But Aporia manages to counter Yusei's strategy, and has his Machine Divine Emperor Mechanicle Infinity Cubic negate the attack, and absorb both dragons, which increases the Machine Divine Emperor's attack points from 4,000 to 10,300. Aporia then uses a trap, which reduced Yusei's life points from 2,800 down to 400, and allows his life points to rise back up from 3,400 to 4,000. However, thanks to the wishes of the Signers, Yusei is able to draw the cards he needs that are in their possession.

Yusei uses the special ability of Black-Winged Dragon to weaken Machine Divine Emperor Mechanicle Infinity Cube's attack points, and Aporia's life points, both down from 4,000 to 2,600. Then, Yusei defeats Aporia, using the combined might of the 3 Signer Dragons, which causes him to crash into the sea. By this, Team 5D's wins the WRGP finals. Then, the red sky returns to its blue color, and the lightning strikes stop. Then, Team 5D's celebrates their victory during noontime. However, their victory is short-lived, as the Infinity Circuit is complete, and the Ark Cradle breaks through the sky from the "distorted dimension," and it begins to descend towards New Domino City.

Sherry reveals that Z-ONE has shown her the future, and insists that Yusei not board the Ark Cradle, revealing she has switched sides to join Z-ONE, since she was convinced that Yliaster's plan was the only was to prevent the global destruction in the future. She also reveals that now having joined Z-ONE, she will do everything in her power to stop him. Despite this knowledge, Yusei still wants to do something to save the city. Sherry then reports to Z-ONE that Yusei did not heed her warning. When Z-ONE asks why she warned him, Sherry simply replies that the warning will cause Yusei to do something, which would allow her to kill Yusei herself, like to promised herself to. is approached by Team Ragnarok who, with the help of Bruno, manage to use the old Ener-D reactor and Nordic Gods to create a path from Daedelus Bridge to the Ark Cradle. Yusei wants to go on his own, but instead, the rest of Team 5D's joins him, with Bruno in his Vizor form following them.

Team 5D's, and their friends all survive the fall, but get separated into three groups: Yusei with Bruno, Crow with Akiza, and Jack with Leo and Luna. The narrow platforms on which they land on are revealed to be routes leading to the three planetary gears powering the main Ener-D generator, and eventually leading to the Center Gear, which was what they are looking for. Vizor tells them that if they don't reach all 3 gears, then they wouldn't be able to reach the Center Gear, and the Ener-D generator of the Ark Cradle would continue to produce negative energy, which would result in the destruction of New Domino City. Crow and Akiza arrive first at one of the 3 gears, which was the one that was closest to them. But then, they are confronted by Sherry, who reveals that she joined Z-ONE, because he offered her the chance to grant her wish, before challenging them to a duel. Sherry then reveals that her wish is that Z-ONE would bring back her happy days with her family.

Sherry reveals that Z-ONE promised to rewrite her past, so that her parents would never have died if she carried out his plans. She uses the Z-ONE spell card to activate the Soul-Binding Gate field spell, which inflicts 800 points of damage whenever any of them try to summon monsters. As Akiza and Crow defend each other from Sherry's attacks, Sherry tempts Crow with the offer of using Z-ONE's power to change the past, so that Zero Reverse would never happen, so that the children of Satellite wouldn't have been orphans, including Crow, Yusei, and Jack, when they were children, if he surrenders and joins Z-ONE. However, Akiza reminds Crow that he should instead fight for their future, as that was what they as Signers should do. Then, they summon their respective dragons, and use their combined strength to defeat Sherry, which causes the 1st gear to stop rotating.

Jack, Leo and Luna reach the second gear, where they are shocked to see that Aporia has survived the crash, and that he is waiting for them. He forcefully attaches devices onto them, which pierce into their hearts whenever they take damage from the duel, meaning that they will die if their life drops to zero, with the only way of removing them is to defeat him in a three-on-one duel. Aporia activates the field spell Fortissimo the Mobile Fortress, and combines with it. Aporia also sets a trap which blasts players with real damage whenever they summon monsters. Although Leo promises to protect Luna and help Jack, Aporia counters each of his traps, making things worse for his allies. Furthermore, Aporia's attacks leave both Jack and Luna in critical states, and leaves Leo in despair.

As Jack, Leo and Luna struggle to survive, Aporia summons his key monster, Machine Divine Emperor Dragon Asterisk which will inflict 1000 points of damage to anyone who tries to Synchro Summon. Lamenting that he hasn't been able to protect anyone, Leo risks some of his own life points to protect Jack and Luna and weaken Asterisk. Leo then summons Power Tool Dragon and Ancient Fairy Dragon and gets hit by the 4,800 points of effect damage, bringing his life down to zero, causing him to die. The shock of Leo's death puts Luna in a critical state, as her life points gradually starts to drop, as her pulse weakens. However, Leo comes back to life with 100 life points, thanks to Ancient Fairy Dragon, and his Morphtronic Lighton's effect, and becomes the sixth and final Signer, with the Mark of the Crimson Dragon's Heart.

Leo uses Life Stream Dragon to counter Asterisk's, and Fortissimo's damage effects, and to restore everyone's life points to 2,000 (not including Aporia), which puts Luna out of the danger of dying. Seeing that his efforts to inflict damage to the Signers has failed, Aporia gets really agitated. Aporia then activates a trap to prevent Synchro Monsters from attacking, but Luna uses Ancient Fairy Dragon's ability to destroy his field spell, and activate one of her own that supports Synchro Monsters, allowing Jack to bring out Scar-Red Nova Dragon. The destruction of Fortissimo causes the fortress' structure to shake violently, and begin to collapse. Aporia manages to bring out Machine Divine Emperor Mechanicle Infinity Cubic to increase Asterisk's attack points, but Leo and Luna use their traps and dragons' abilities to weaken it. Jack then destroys Asterisk by attacking with Scar-Red Nova Dragon, which defeats Aporia, who falls to his "doom" with a feeling of hope in his heart.

Yusei not only has to deal with Antinomy, but also the flames coming from the star. Antinomy brings out his Accel Synchro monster, Tech Genus Blade Blaster, and deals a lot of damage to Yusei. Antinomy talks about how he was a champion Turbo Duelist, before the Machine Emperors destroyed the world. He was rescued by Z-ONE (who is actually the future version of Yusei), before Antinomy could commit suicide by letting a Grannel kill him. Seeing that Z-ONE still had hope (before the events of the Ark Cradle), and that he had none, Antinomy felt shame, and joined Aporia and Paradox as one of the 4 remaining survivors. He then lived his life working with Z-ONE on his experiments to save humankind (which failed), before being revived as a cyborg, after his human body died, whose mission was to teach Yusei the Accel Synchro, in order to provide the power needed to bring Ark Cradle to New Domino City.

Yusei is put in a desperate situation, as Tech Genus Halberd Cannon brings his life points down to 100, and keeps him from summoning monsters. Furthermore, the Black Hole becomes more organized, and begins to approach from behind, threatening to suck Yusei in if he falls behind. However, Yusei manages to summon out Balance Shooter, which gives Shooting Star Dragon the power to overwhelm Halberd Cannon and defeat Antinomy. The impact of the attack causes a part of Antinomy's glasses to break. As they are sucked into the black hole, Antinomy asks Yusei to master the Delta Accel Synchro and save the world, and remembers his fond memories as Bruno, back when he was still Yusei's friend. Remembering this, Bruno tosses Yusei his broken glasses, and then he sacrifices himself to get Yusei out of the black hole, and back to the Ark Cradle. Then, the 3rd gear stops spinning, and Yusei grieves over the loss of Bruno, who was once his friend.

With the 3rd gear stopped, the Signers gain access to the Center Gear, and Yusei rejoins the others, telling them the truth about Antinomy, and about the Delta Accel Synchro method. They continue onwards to the center of the Ark Cradle, where they spot more, but smaller gears, as well as the Ener-D Generator that was called the Center Gear, which was powering most of the negative Ener-D of the Ark Cradle. Then, they enter a room with blue walls, located at the very heart of the Ark Cradle, where ZONE awaits them. Z-ONE reveals he was behind the Zero Reverse incident, as well as Paradox's scheme, to try to stop the existence of Synchro Monsters, and Ener-D. Z-ONE then decides to settle things in a duel, and if Yusei wins, the Center Gear would stop working (the Center Gear is really the key Ener-D generator, which is the main source of power for the Ark Cradle's overall Ener-D Generator), and the Ark Cradle would disappear for real.

Aporia summons Machine Emperor Skiel by destroying Sky Core, but then destroys it using a trap, so he can draw the spell card "Destroyed Future." Then, Aporia activate its effects, choosing to destroy his own deck, so that he can use his card, After Glow, in an attempt to guarantee a win against Z-ONE. However, on his next turn, Temporal Machine God Metaion returns to Z-ONE's deck, and he summons out another Temporal Machine God, Razion, using Zero Machine Ein's effect once more. Razion's effect returns all of Aporia's cards in his Graveyard back to his deck, which was then suffled. As a result, Aporia is unable to draw the card he needs (After Glow), and is defeated by Razion's effect, which deals him 1,000 points of damage when he draws a card on the draw phase. Before he dies, Aporia gives Yusei's Duel Runner wings, by fusing his duel disk with Yusei's duel runner, allowing it to fly.

Yusei summons out both Red Dragon Archfiend and Black-Winged Dragon, whilst Z-ONE replaces Metaion with Razion, using his trap, Zero Machine Ein, which allows him to summon a Temporal Machine God without any releases, but will lower its attack points to zero. Z-ONE then activates Razion's ability when Yusei draws a card on his turn, reducing his life points to 3,000. The damage sends Yusei flying out of control. But before he smashes into the Ark Cradle, Yusei manages to regain control of his duel runner, and fly back to Z-ONE. Yusei then summons Black Rose Dragon, and uses a trap to negate its effect and deal damage to Z-ONE, reducing his life points to 1,500. Z-ONE then spins out of control, and when he smashes into a building of the Ark Cradle, the impact causes the right half of Z-ONE's mask to break, revealing his face to be that of a much older looking Yusei.

Z-ONE claims to be Yusei from the future, though Yusei refuses to believe this. Z-ONE sacrifices Zero Machine Ein to activate Infinite Machine Ein Soph, a trap that allows him to summon more than one Temporal Machine God at a time with any releases, but will still lower their attack points to zero. Z-ONE then summons 3 more Temporal Machine God monsters through his trap's effect. He then attacks Yusei's Black-Winged Dragon with his Temporal Machine God Tzaphion, in an attempt to utilize its ability, which would send all of Yusei's traps on his field back to his deck. Yusei however, counters this, activating Scap-Iron Scarcrow, saving himself from the attack. Z-ONE then attacks with the other 2 Temporal Machine Gods, using their abilities to restore his life points to 4,000, with Zadion's effect, to return Yusei's monsters to his deck, and to deal him damage, with Camion's effect, which reduces Yusei's life points to 1,500.

Yusei uses Shooting Quasar Dragon to destroy all 5 of Z-ONE's current Temporal Machine Gods, and then manages to bring out Shooting Star Dragon to deal a lot of damage to Z-ONE, reducing his life points to 700. Z-ONE screams when he takes the damage, and then he crashes into New Domino City's central building. Yusei then removes all of his speed counters to draw Clustering Wishes, and sets it face-down. After Yusei and Z-ONE talk about the right of changing the future, Z-ONE angrily blasts a hole in the building, and flies back up into the sky. Z-ONE then feels angry at Yusei, for reducing his life points by such a great amount, and tells Yusei that he will now prove to him that hope, and the possibility to fix the future without New Domino City's destruction, which Yusei believes in, was nothing before his power.

A few years have passed since Z-ONE's defeat. The Public Safety Maintenance Bureau has dissolved into a city hall, with Lazar becoming the city's mayor. Yusei has become a scientist who supervises the completion of a new Ener-D mainframe, titled Fortune, to ensure the safety of the city. Crow had become a highway patroller getting an invitation to an overseas leagues, Akiza plans to study abroad to become a doctor, and Leo and Luna receive a mail from their parents asking them to leave New Domino City to live with them, leading everyone to wonder about the future of Team 5D's. Jack arrives after training with (defeating) several other duelists, wanting to leave New Domino City for a World League, in order to fulfill his dreams of becoming the World Duelist King, and Yusei challenges him to a duel, to decided the Signers' futures.