Plot
In Paradise City's You Show Duel School, a second-year middle school student named Yuya Sakaki aspires to become a professional Dueltainer, he believes that Dueling is for fun and should be enjoyed just like his father, who disappeared. Yuya awakens a new power called Pendulum Summoning, which attracts the attention of the Leo Corporation's president, Declan Akaba. Yuya later meets three Duelists who greatly resemble him: The collected Xyz duelist "Yuto" from the Xyz dimension, whom he unknowingly absorbed during the Duel between Yuto and Yugo. The overconfident Synchro duelist "Yugo" from the Synchro dimension, with a similar background with Yusei in Yu-Gi-Oh! 5Ds (also uses a dragon that resembled Yusei´s Stardust Dragon). And the sadistic Fusion duelist "Yuri" from the Fusion dimension, who works for the Professor in Duel Academy, turning people into cards.
These look-alikes originate from other dimensions besides Yuya's Standard Dimension as he and his friends find themselves in the middle of an interdimensional conflict against the Fusion Dimension's Duel Academy, which Yuri attends. Duel Academy is led by Declan's estranged father Leo, who seeks to unite the four dimensions. Leo formed a group of elite duelists called the Lancers (includes Yuya, Moonshadow & Shay) to stop his father, while they build their numbers while traveling to the Synchro and Xyz Dimensions to find Yuya's friend Zuzu Boyle. The group is joined by the Fusion Dimension's Celina, who resembles Zuzu.
The Lancers were aware of the Four dimensions and went to the Synchro dimension where Yugo hails from, Yugo was heavily convinced that Zuzu was his abducted childhood friend Rin. A threat arose from the head of sector security in the Synchro dimension, the head of sector security was mind controlling all of sector security, but after Yuya defeated Jack they were able to stop it but they ended up in the Xyz dimension were Yuya meets a student of Duel academy who dueled his father but failed to turn him in to a card, Yuya was more convinced that his father was alive.
Gradually recognizing a dark presence swelling inside him since absorbing Yuto, Yuya learns he has a strong psychic connection to him, Yugo, and Yuri that occurs whenever their summoned dragons are calling one another. Yuya and his friends also realized that Leo seeks to capture Zuzu and Celina, the professor already having Rin and the Xyz Dimension's Lulu Obsidian in his custody. Once in the Fusion Dimension to save Celina, Zuzu gets captured as well and Yuya is reunited with his father as the Lancers infiltrating Duel Academy to save the girls. When they confront Leo, he reveals the four dimensions used to be one world until the day a duelist named Zarc attempted to destroy everything. The Professor intended to stop Zarc with the special En Cards he created. His daughter, Ray, steals the cards and sacrifices herself to defeat Zarc but the Four En cards had an effect that splits Zarc and Ray with the original dimension into four worlds.
The Professor reveals that Zarc is the darkness within Yuya and his counterparts, who are themselves remnants of Zarc's scattered essence, which has been compelling them to absorb each other so Zarc can be reconstituted and exact his revenge. Only Ray, who has been reincarnated as Zuzu and her counterparts, had been subconsciously preventing Zarc's attempts to reawaken prior to The Professor having the girls abducted. The Professor intends to merge them back into his daughter and reunite the 4 dimensions into the Original Dimension using his Arc-V Reactor. But the reactor is unable to fully restore Ray's physical form as The Professor planned due to lack of life energies, so the Professor decided to send Duel academy the three dimensions to turn people in to cards to power up the Arc-V Reactor. After Yuri dueled Yugo, he won and absorbed Yugo, Zarc capitalized on the turn of events by taking over Yuya's body and having him absorb the willing Yuri to complete his resurrection. Yuya's friends all proceed to challenge Zarc in a series of two-on-one duels to stop him while reaching out to Yuya. With Ray possessing Declan's younger sibling, Riley, to fight Zarc, Yuya manages to regain himself to help Ray defeat Zarc with the En Cards that splits the dimensions once more.
When Yuya awakens in the Standard Dimension that has been reborn as the Pendulum Dimension, he had no memory of his experience across the dimensions or of Zuzu until Declan restored everyone's memories with a reenactment of the Arc League Championship. Declan reveals that Riley used a moment in the dimensional divide to transfer Zarc's essence from Yuya into herself to keep the evil spirit from being scattered across the dimensions again, with Riley turned into a catatonic infant as a result. Declan fears that Zarc may eventually take over Riley's body and resume his rampage again. Yuya is told that only he, as Zarc's essence, can stop Zarc for good by using his Dueltaining skills to make Riley smile and pacify the possessing spirit. Yuya proceeds to travel to other dimensions and defeat the other Lancers with Riley watching the footage. On his way, Yuya finds Zuzu and her counterparts still inside the Arc-V Reactor in an inactive state. Though his counterparts help him tame the Four Dragons, Yuya learns he made no progress with Riley. He convinces Declan to let him take the professional duelist test right after he got promoted into Senior class, with Declan as his opponent. Learning who Zarc was in his life, Yuya and his counterparts manage to defeat Leo and pacify their past counterpart. This act awakened Ray, who appears in the Pendulum Dimension and revives as Zuzu, with her counterparts now a part of her, similar to Yuya's case. The two of them are reunited at last, and the four dimensions were connected and the Standard was known as the Pendulum dimension. With the help of Yuto, Yugo & Yuri who were a part of Yuya, Yuya managed to make Riley smile. The series ends with Zuzu restored, with her counterparts existing inside her like Yuya is and his counterparts.
