Plot
In Paradise City's You Show Duel School, second-year middle school student Yuya Sakaki aspires to become a professional Dueltainer, believing 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, who has a similar background with Yusei in Yu-Gi-Oh! 5Ds (and uses a dragon that resembles 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, and he and his friends become involved in 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. Declan forms a group of elite duelists called the Lancers, whose members include Yuya, Moonshadow, and Shay, to stop his father. They increase their numbers while traveling to the Synchro and Xyz Dimensions to find Yuya's friend Zuzu Boyle, and are joined by the Fusion Dimension's Celina, who resembles Zuzu.
Aware of the four dimensions, the Lancers go to the Synchro dimension where Yugo hails from, as Yugo is convinced that Zuzu is his abducted childhood friend Rin. A threat arises from the head of sector security in the Synchro dimension, who is mind controlling all of sector security. Yuya defeats Jack and they are able to stop it, but they end up in the Xyz dimension. There, Yuya meets a student of Duel Academy who dueled his father but failed to turn him into a card, and becomes more convinced that his father is alive.
Gradually recognizing a dark presence that has been swelling inside him since absorbing Yuto, Yuya learns that 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 realize 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 is captured as well and Yuya is reunited with his father as the Lancers infiltrate Duel Academy to save the girls. When they confront Leo, he reveals that the four dimensions used to be one world until the duelist Zarc attempted to destroy everything. The Professor intended to stop Zarc with the special En Cards he created, but his daughter, Ray, stole the cards and sacrificed herself to defeat Zarc. The effect of the Four En cards split Zarc and Ray and split 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 four dimensions as the Original Dimension using his Arc-V Reactor. However, as the reactor is unable to fully restore Ray's physical form as The Professor planned due to a lack of life energy, he decides to send Duel Academy to the three dimensions to turn people into cards and power up the Arc-V Reactor. Yuri duels Yugo and absorbs him after winning, but Zarc capitalizes 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 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 control and help Ray defeat Zarc with the En Cards, causing the dimensions to be split once more.
Upon awakening in the Standard Dimension, which has been reborn as the Pendulum Dimension, Yuya does not remember his experiences across the dimensions or Zuzu until Declan restores 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 prevent him from being scattered across the dimensions again. This caused Riley to turn into a catatonic infant as a result, and Declan fears that Zarc may eventually take over Riley's body and resume his rampage. Yuya is told that he, being Zarc's essence, is the only one who can stop Zarc for good by using his Dueltaining skills to make Riley smile and pacify Zarc. Yuya proceeds to travel to other dimensions and defeat the other Lancers, with Riley watching the footage. Along the way, Yuya finds Zuzu and her counterparts dormant inside the Arc-V Reactor and tames the Four Dragons with help from his counterparts. After being promoted to Senior class, Yuya convinces Declan to let him take the professional duelist test, with Declan as his opponent. Learning who Zarc was in his life, Yuya and his counterparts defeat Leo and pacify Zarc. This awakens Ray, who appears in the Pendulum Dimension and is revived as Zuzu, with her and Yuya's counterparts existing inside them as part of them. They are reunited at last, and the four dimensions are connected. With help from his counterparts, Yuya manages to make Riley smile.
