Seasons & episodes

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.

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?