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.

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.

As Yusei and Crow work on their new engine, they are visited by Leo, Luna and their classmates, including the timid Sly, who is nearly tempted to steal Stardust Dragon. Yusei is asked by the Academy's principal to fix something, which turns out to be the head instructor, Rudolph Heitmann, who is threatening to expel Leo, Luna, and their friends for using low level monsters. Yusei arrives, and challenges Heitmann to a duel, in order to stop them getting expelled, and to prove the strength of low level monsters. Heitmann manages to summon three Ancient Gear Golems on his first turn and deals a lot of damage. Yusei summons out Stardust Dragon, but sacrifices him to summon out several Tuner monsters, which belong to the relevant students. Yusei manages to use them to defeat Heitmann, who learns his lesson, and withdraws the expulsions. As Yusei leaves, Sly contemplates to steal Stardust Dragon. Fortunately, he will never get that chance.

The mysterious dueler, known only as Vizor, decides to train Yusei to face Ghost. He starts off by racing him, testing Yusei's ability to handle mach speeds. Once he cleared that, the duel begins, with Vizor managing to summon two Synchro Monsters in his first turn. Before Yusei is able to counterattack, Vizor speeds up to mach-speed, performing an Accel Synchro with his two monsters to form a new one. Yusei responds by summoning Drill Warrior, and powers it up later, though Vizor decides to take direct damage and lose the duel, instead of damaging his monster. The Yliaster, who had been watching the duel, become curious about Vizor's actions.

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.

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.

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.

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.