Yusei is transferred to a different cell, away from Yanagi. His new cellmate, Alex, plans to escape and offers to take Yusei with him, but he refuses to leave without Yanagi and Tanner. Meanwhile, Armstrong has been harassing Tanner, and Yusei ends up in a duel against him, using a deck built with treasured cards given to him by all the other prisoners.

Yusei is caught in Armstrong's trap - not only is he forced to discard ten cards each turn, each Life Point lost also delivers a painful electric shock. Armstrong has disabled the electric current to his own Duel Disk, and thus does not feel any pain, until Alex breaks into the control room. He starts the current flowing again, but Armstrong just gets back up and keeps going. Despite the overwhelming odds, Yusei is able to pull through and win the duel. He is allowed to leave the prison.

The first day of the Fortune Cup comes to a close. The audience attention is cast to an image of Krieger, who shall face Yusei tomorrow. As Tanner says that he wonders what kind of Duel Runner Krieger uses, something comes to Leo's mind, causing him to run off.

Krieger successfully summons Flying Fortress SKY FIRE and uses its effect to prevent Yusei to play his cards right. What Yusei doesn't know is that Krieger holds Goodwin responsible for the destruction of his home village.

Yusei wins his match against Akiza, but feels reluncant about it since he couldn't help her as much as he would have wished. He then rushes to Goodwin's tower in order to rescue his friends, but what he finds is Jack along Goodwin, and he explains how his rivalry with Yusei all began. Shortly after, the final duel between Jack and Yusei takes place, and to Yusei's surprise, his friends from Satellite are safe and sound, freed from the container that served as prison in Satellite, and they all watch Yusei as he duels.

The Fortune Cup Finals continue as Yusei summons Stardust Dragon to battle Jack’s Red Dragon Archfiend. As the battle goes on, the Crimson Dragon appears and Goodwin, revealing that he is the fifth signer and has a severed arm in a tank with the final Signer Mark shows Yusei, Jack, Akiza, and Luna bizarre visions of the People of the Stars and the future of New Domino City, being engulfed in a Spider shaped geoglyph of fire.

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

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

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

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

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

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

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

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

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

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.

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.

Recap episode. As Yusei tests out his engine, Jack and Crow look back on his previous battles to try to understand him. When they meet up with Yusei, he suspects that Yliaster is the one behind Ghost and is planning something big with the WRGP. He also tells Jack and Crow about Accel Synchro. They become determined to learn this new move, which would require a new engine. Meanwhile, a mysterious person washes up on the beach.

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.

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.

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.

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.

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.

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.

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.

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.

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 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.

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.

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.

The duel between Yusei and Jack finally comes to an end. Which of them will claim victory? And what shall become of the Signers as they prepare for their futures?