Frieden ist nach dem Sieg über die Finsteren Auserwählten in New Domino City eingezogen. Jedoch hält dieser nicht lange an, denn ein neuer Bösewicht namens Ghost tritt in Erscheinung. In einem ersten Duell gegen den durchgedrehten Duellanten verletzt sich Trudge schwer. Daraufhin machen sich Yusei, Jack und Crow auf die Suche nach Ghost.
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. Jack, Yusei and Crow, meanwhile, are preparing for an upcoming tournament, the World Racing Grand Prix (WRGP), but when Trudge suggests Jack, Crow, and Yusei to help him take down the Ghost, Crow rejects Trudge's plea for assistance, in favor of working on their new engine, as he states that they have the Grand Prix to prepare for, and that they don't have any time to spare. Instead, Crow insists that Trudge and the rest of Sector Security, being the cops, go chase after the Ghost themselves. Trudge encounters Ghost later that night, but is defeated and severely injured. He warns Yusei not to use Synchro Monsters against Ghost, as "Synchros are useless." After the incident, Crow feels guilty about what he told Trudge. After Yusei tells him that blaming himself was not going to work, Crow asks Yusei what he should do, to which Yusei replies that they go find and beat the Ghost. Yusei, Jack and Crow then go and search for Ghost, who Yusei soon encounters after several hours of riding. He soon finds himself up against Ghost's ace monster, Machine Empero
Six mois après la bataille contre les Pactisants des Ténèbres, une pierre tombe du ciel en périphérie de la ville. Lazar s'y rend pour enquêter et se retrouve face à trois personnes venant d'Yliaster. Trudge et Mina eux, enquêtent sur un duelliste nommé Ghost qui fait crasher ses adversaires après les avoir battus. Ils demandent de l'aide à Yusei, Jack et Crow qui préparent un nouveau tournoi mondial, mais Crow refuse de les aider. Trudge part donc à la recherche de Ghost et le rencontre. Ils s'affrontent en duel et Ghost le bat. Plus tard dans la nuit, Yusei, Jack, Crow et Mina se rendent à l'hôpital pour voir Trudge et Yusei décide d'aller affronter Ghost lui-même. Il le retrouve et l'affronte, cependant, Ghost invoque un monstre Empereur Machine qui a pour but de détruire les monstres synchros.
ゴドウィンとの激しい戦いから半年後、ネオ童実野シティは大きな変化を遂げていた。シティとサテライトの境界がなくなり、人々の心は街の復興に向けてひとつになり始めていた。そんな時、治安維持局ではイエーガーが新任の長官の到着を今や遅しとイライラしながら待っていた。そこへシティ郊外に巨大な隕石が落下したという報告が入り、急いで現場へ向かうのだが・・・・。
