He Dueled against in the second day of the Friendship Cup, and his entrance was booed by the crowd. Yuya attempted to protest against the Friendship Cup for sending the losers to do forced labor, but to his utter shock neither the crowd of Commons nor saw anything wrong with that. 227 urged Yuya to either Duel him or surrender, and Yuya traded blows with the Duel Chaser's "" Synchro Monsters, but briefly hesitated before making a game-winning attack with "Odd-Eyes Pendulum Dragon", allowing 227 to seal Yuya's attacks with "". To his surprise, 227 brought out a Fusion Monster, "", and took control of most of Yuya's field. The crowd's bloodlust for battle rather than entertainment briefly set Yuya off, causing his eyes to glow in their . Yuya then consciously Special Summoned "", used its effect to destroy "Goyo Emperor", reclaimed control of his monsters, then brutally attacked with "Odd-Eyes Pendulum Dragon" for the win, deliberately knocking 227 off his Duel Runner. Initially downcast at the win, Yuya attempted to stop the staff from taking the injured 227 away. He was returned to his room by Sam, and didn't pay attention to the next Duel between Yugo and Sylvio until Yugo Synchro Summoned "". Yuya's "Odd-Eyes Pendulum Dragon" began to react to "Clear Wing", and Yuya began mimicking Yugo's moves and words, while during the Turbo Duel, Yugo took on some of Yuya's mannerisms. The effects ended after Yugo was victorious, and Yuya watched helplessly as Sylvio was taken away.
Yuto and Yuya called off the Duel, and Yuto explained about the four Dimensions to Yuya. Yuya was skeptical, but told Yuto that Dueling shouldn't be used for fighting as it was by the other Dimensions. They were interrupted by the arrival of a Duelist on a , who crashed into a streetpost, and revealed that he too resembled Yuya and Yuto. Introduced as a Pawn of Fusion, the Duelist stated that his was , and he quickly challenged Yuto to a Duel. Yuya watched the Duel in shock as the Duelists ran around agily, and experienced the same burning sensation when Yugo, a user, called out "." The sensation intensified when Yuto retaliated with "Dark Rebellion Xyz Dragon," causing the two Duelists to become possessed and violent. Yuya managed to calm Yuto down, getting him to call off his attack, but was unsuccessful in calming Yugo, who proceeded to claim victory. Yuto saved Yuya from the shockwave, and Yuya ran to his defeated doppelganger, begging him to stay with him. Smiling, Yuto handed Yuya his glowing "Dark Rebellion Xyz Dragon," asking Yuya to use his power to bring Duels with smiles to the world, and both he and Yugo vanished in a glow of blue light. Yuya sat there in shock, collapsing as Zuzu arrived.
Barrett used his Trap Cards, "" and "", to seal Yuya's attacks and lower his LP. Throughout their Duel, Barrett tried to convince Yuya to give up and divulge Zuzu's location and Celina to return with him. Yuya refused to comply and repeated his resolve and determination to prevent Celina's and Zuzu's capture. When the Obelisk Force tried to capture Celina, Sora saved her but arrived with three more Obelisk Force soldiers to capture both of them, Yuya was surprised to see his final counterpart. Yugo arrived as well to Duel Yuri and when they Summoned "Clear Wing Synchro Dragon" and "", the presence of the caused Yuya, Yuto, Yugo, and Yuri to a enter synchronized Berserk Mode again. While synced, Yuya and his counterparts start shouting that they waited for this time to become one and for a revival. But when Zuzu arrived her bracelet teleported Yuri and Yugo away, and returned Yuya to his senses. Yuya became upset when he realized that Zuzu was with him, knowing that the situation got worse since what Duel Academy wanted is now in front of their eyes. Barrett saw the pointlessness of the Duel and offered to end it, but decided to go on, touched by Yuya's actions and bravery. This also caused Barrett to gain respect for Yuya's resolve. Their Duel got interrupted by Sergey, who trapped Zuzu with his , "".
Yuya has the ability to with his dimensional counterparts, though the exact circumstances are unknown. Unlike the apparent synchronization that Yuto and Yugo previously displayed, he has complete sync with his counterpart(s), capable of seeing and experiencing everything that they experience. In this state, Yuya and his counterpart(s) act as if they were one person, speaking, moving, and responding in the exact same manner. When the Duel ends, both of them were unable to understand what had happened in that brief period of time, though both retain the memory of the Duel occurring. Yuya is capable of retaining his own thoughts while in sync though he gradually loses the ability to distinguish between himself and Yugo, as seen when he worried that his victory would send Sylvio to the underground facility when it would have been Yugo's victory that would do the deed. After Yugo's Duel with Celina, Yuya has become aware of this ability. During his Duel with Crow, he synchronizes with Yuto, Yugo, and after Roger uses the he planted in Yuya's helmet at maximum. The action also cause hime to go berserk.