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.

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.

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.

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 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.

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.

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.

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.