The third installment in the franchise of Yu-Gi-Oh! anime series.
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, Jack and Crow finally complete their new Duel Runner engines, and they name their WRGP team Team 5D's. They have a practice run on the WRGP circuit. However, Crow refuses to stop when the practice session is over, and causes one of Team Unicorn's members to crash. As a way of apology, Yusei accepts a supposedly friendly duel with their "best" duelist, Andre. Unbenownst to Yusei, the duel is really a means to learn his strategy. Andre gets a head start with his Green Baboon, before Yusei summons his Junk Archer. However, Andre responds by bringing out his Behemoth, putting Yusei in a tight spot.
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 manages to destroy Andre's key Speed Spell card, but in doing so allows Andre to activate that, despite knocking himself out, takes a huge chunk out of Yusei's life points. Yusei then faces Team Unicorn's next duelist, Breo, who soon summons his Synchro monster, Voltic Bicorn. He soon destroys it however in order to implement his deck destruction tactic.
Breo manages to destroy Stardust Dragon and leave Yusei with just five cards left. Yusei soon summons Junk Destroyer and knocks Breo out, leaving him just 1000 life points and four cards to face against Team Unicorn's final member and leader, Jean. Jean summons out Lightning Tricorn, but Yusei manages to avoid losing to Speed World 2's effects. However, Jean soon destroys Yusei's monsters and launches a direct attack at him.
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 reveals that Taro's plan is to sacrifice a level 1 monster that has been on the field for ten of his turns so he can summon his trump card, Zushin the Sleeping Giant. When the crowd gets word of this, they start cheering for Team Taiyo, along with the people from their hometown. Crow's attempts to destroy the sacrifice fails, allowing Taro to summon out Zushin, which defeats Crow. Yusei takes over, and brings out Stardust Dragon to battle against Taro.
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.
Jack gets the truth behind the fixed duels out of Lazar, who confirms what Dragan had told him. Jack becomes irritated as a result, so Yusei suggests he use the WRGP duel to regain his pride. In the match between Team 5D's and Team Ragnarok the next day, Jack and Dragan start off, and are surprised to find out that their starting hands are the same as their previous duel. Realizing the chance to do things properly, the two replicate their first turns from that match, this time, with Dragan being able to use his trap card, which Jack counters with his own. Dragan then brings out his Aesir, Thor, which manages to destroy Jack's Red Dragon Archfiend.
As Dragan continues his attack, Jack starts to take real damage from Thor. However, Jack starts to make a comeback and summons out Red Nova Dragon. However, Dragan activates traps which weaken Red Nova Dragon, and protects Thor. Jack manages to pull off a tactic to return Red Nova Dragon to its full power, destroying Thor and defeating Dragan. However, before he loses, Dragan revives Thor and deals damage to Jack.
Ragnarok's 2nd turbo duelist, Broder, takes over and uses Thor's special abilities to knock Jack out. Crow enters the fight, but his attacks prove ineffective against Broder's traps, and he takes a lot of damage from Thor's attacks. Noticing the support Crow gets from the children, Broder explains how he came across a similar group of children, expressing his desire to fight Yliaster in order to protect them. Crow brings out Black-Winged Dragon, but Broder brings out his Aesir, Loki, which destroys Crow's Black-Winged Dragon.
With just 50 life points left, Crow's supporters almost get into danger while trying to cheer him on, reinvigorating Crow's resolve, and he soon manages to revive Black-Winged Dragon. Then, Crow activates a trap card from the Graveyard, which clashes with Broder's trap, knocking them both out. Yusei begins his round against Halldor, who quickly summons his Aesir, Odin.
Yusei must now face the power of Halldor and all three Aesirs. As Yusei expresses his desire to defeat Yliaster and see his father again, he gains the Seal of the Crimson Dragon, and summons out Majestic Star Dragon. However, Halldor manages to learn Yusei's strategy, and executes a successful counter. Halldor then activates a continuous trap card from his Graveyard, Gjallarhorn.
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.
Despite the others' concern for his safety, Crow goes to face Jakob. Crow attempts a technique to utitlize his Synchro Monster's abilities without putting them at risk, by summoning Blackwing Aurora of the Northern Lights, and by activating its special ability, but Jakob counters Crow's stragety by using Scar-Red Nova Dragon as a shield, and by attacking him 2 times with Jack's dragon. Crow is then defeated by Jakob, but manages to summon Black-Winged Dragon in defense mode for Yusei to use, by playing a trap card, after being attacked by Machine Emperor Grannel Infinity. Crow then crashes, and Yusei goes out to face Jakob.
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.
Temporal Machine God Sandaion's attack points are then lowered from 4,000 to 0, by the effects of Infinite Machine Ein Soph. When Z-ONE attacks Yusei's Ancient Fairy Dragon with Temporal Machine God Michion, Yusei's life points are reduced to 750, by Michion's ability. As a result of the damage, Yusei's duel runner plunges down again, but Yusei is able to navigate through the structure of the Ark Cradle, and find his way back to Z-ONE. But when Z-ONE attacks with Hanion, and then Raphion, Yusei is able to protect himself from taking damage, and losing to their effects, by timing the activation of Scrap-Iron Scarecrow, and his Synchro Believer's ability.
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.
Yusei summons Nitro Warrior, but Jack manages to counter its attack and summon out Exploder Wing Dragon to destroy it, though Yusei manages to beat it with his Turbo Warrior. As the others watch the duel, they recall how Yusei had managed to change their lives. Jack then brings out Crimson Blader, which destroys Turbo Warrior and prevents Yusei from summoning more monsters during his next turn, but Yusei manages to survive Jack's attacks before Stardust Dragon and Red Dragon Archfiend return. Jack then summons out Red Nova Dragon, with a power of 6,000 attack points.
Several years into the future, Luna and Akiza are moving on with their careers whilst Leo, Jack and Crow continue to make strides in the Turbo Duel circuit. Back in the present, Yusei summons out Shooting Star Dragon and destroys Crimson Blader. Jack then activates the continuous trap card, Scar-Red Cocoon, and equips it to his dragon, which prevents Red Nova Dragon from being destroyed in battle. Later, after surviving a few of Jack's attacks, Yusei uses a trap so that Shooting Star Dragon can destroy Red Nova Dragon, along with itself. Jack then activates Scar-Red Cocoon's second effect; since Red Nova Dragon was destroyed while it was equipted with Scar-Red Cocoon, he can special summon Red Dragon Archfiend during his end phase. With both Red Nova Dragon and Shooting Star Dragon sent to the graveyard, and Red Dragon Archfiend back on the field, Yusei then brings out Junk Warrior, and uses a trap to summon a few low level monsters to the field.