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Interdimensional War is the term used to refer to the prolonged hostilities between the Fusion Dimension and the Xyz Dimension. It consequently serves as the main conflict of Yu-Gi-Oh! ARC-V and stems from Duel Academy's Head Professor Leo Akaba's desire to "unite all worlds", and this goal is referred as "Arc Project".
Sometime prior to the beginning of Yu-Gi-Oh! ARC-V, Leo Akaba stepped down from the presidency of the Leo Corporation in the Standard Dimension and became the Head Professor of Duel Academy in the Fusion Dimension. There, he sent an army of Fusion users to invade the Xyz Dimension, all with the intention of uniting the worlds. In order to facilitate the invasion, Dennis McField was sent to scout Heartland City for Lulu Obsidian, who Leo wanted captured. Once found, the invasion proceeded with the complete annihilation of the Xyz Dimension. In the wake of the invasion, a resistance was formed by the survivors of the dimension, who rallied together in order to repel their attackers. Sometime after this, Lulu was successfully captured by Yuri, causing Shay Obsidian and Yuto to turn their attention to the Standard Dimension in search of clues to her whereabouts.
Upon learning of Zuzu Boyle's existence from Sora Perse, who had been sent to the Standard Dimension for reconnaissance, Leo sent Yuri to capture her. Unknown to Leo, Celina escaped to the Standard Dimension along with Barrett at the same time in an attempt to prove her worthiness of being a Duel Soldier for the Fusion Dimension forces. Upon learning this fact from a defeated Barrett, Leo then sends Sora and a battalion of the Obelisk Force to Paradise City to return Celina to Duel Academy. Both teams eventually failed in their mission, with Zuzu escaping to the Synchro Dimension with Yugo and Celina successfully defended by the soon-to-be members of the Lancers.
During the Lancers' journey to the Synchro Dimension, Dennis who had been working undercover as a spy in the Lancers was discovered and returned to Duel Academy to recuperate by Sora, who had begun to harbor thoughts of defection upon learning of Leo's interest in capturing Zuzu. Upon learning from Dennis that both Zuzu Boyle and Celina were in the Synchro Dimension, Leo Akaba sent Yuri, Barrett and twenty Obelisk Force soldiers to invade the Synchro Dimension. Similar to the attack in Paradise City in which retrieval of the targets was the only objective, only small numbers of Fusion users were sent to New Domino City.
This time, though, with most of the Lancers separated and kept at the Underground Labor Facility, it became more difficult to defend both Zuzu and Celina. Against the advice of the kids that were looking after her, Zuzu escaped from the Underground Facility, where she had been hiding, and went to successfully find Yuya Sakaki. Meanwhile, thanks to Crow Hogan, the defeated Lancers of the Friendship Cup learned of the small invasion and successfully escaped, but they were too late. At the same time the events at the Underground Facility took place, Riley was too tired and traumatic to defend Celina, and Yuya was locked in a difficult battle with Barrett. Sora appeared and declared his alliance with Yuya, but he was only able to prevent Celina's capture by a little more time. Jean-Michel Roget, head of Sector Security, turned out to be a traitor of Duel Academy who intended to use Celina and Zuzu as his lifeline to save himself in case his plans go wrong and his betrayal exposed to Professor Leo Akaba and thus wants both girls captured. Roget sent Sergey Volkov to the girls' location and ordered their capture. In the duel that followed, Barrett experienced defeat in the hands of Sergey. But to Yuya, Zuzu, and Sora's dismay, Barrett successfully activated the dimensional travel app in his duel disk and managed to succeed in escaping and took Celina away with him. Then Yuya tried to protect Zuzu from capture, but even with Sora and the recent arrival of Moon Shadow, Sergey captured Zuzu. Duel Academy's mission ended with partial success.
Then, Roget's plans to takeover the Synchro Dimension ultimately failed and he began his attempt to escape to Duel Academy and save himself through Zuzu. Declan successfully blocked his way while Jack and Crow, the Lancers' most reliable Synchro allies, created a chance to rescue Zuzu. Unfortunately, Roget resorted to his last ditch plan to teleport New Domino into the void between dimensions and capture the Lancers for the Professor Leo Akaba. He activated his own interdimensional transport machine, but just like his plans, they malfunctioned and failed and he got pulled into a wormhole. His fate became unknown.
Unfortunately, a second wormhole opened up and separated Zuzu, Yuya, Shay, Gong, and Sylvio from the rest of the Lancers, Sora, Jack, and Crow. Declan at this point had no way of knowing which dimension they would end up in. Zuzu arrived at the Fusion Dimension, and rest arrived at the Xyz Dimension.
At City, Zuzu learned of the omnipotent status Duel Academy held in the Fusion Dimension. She was able to escape capture from Duel Academy's Juvenile Officers who mistook her for a fugitive thanks to Alexis Rhodes' intervention and reunited with Yusho Sakaki, Yuya's father who went missing three years ago, at the Fusion Dimension's You Show Duel School. It was revealed that Yusho was closely connected to the events before the current timeline.
In Heartland City, Yuya saw through his eyes the consequences of Duel Academy's invasion. He, Gong, and Sylvio rescued a few survivors of the invasion from Duel Academy soldiers who were determined to turn every single survivor into cards. Around this time, he was able to talk to Yuto more often and with a freedom compared to previously. His group of Lancers Dueled against Kite Tenjo, and joined the surviving Resistance members. At the hideout, they found out about the second, debilitating offensive Duel Academy undertook in Shay and Yuto's absence as well as Kite's personal tragedy. To Yuya's shock he also learned about his father's visit three years ago. This led to Yuya searching for his father, and he encountered Aster Phoenix, commander-in-chief of the Duel Academy's forces, and both Yuya and Yuto dueled him that ended in a DRAW.
Having detected the presence of Pendulum Summoning in the Xyz Dimension, according to the deputy commander Mamoru Noro, Duel Academy sent the Tyler sisters over. They encountered Allen Kozuki and Saya Sasayama, mistaking the two Resistance members for Lancers and initiating a Tag-Team Duel with them. Allen and Saya were defeated, and about to be sealed when Sylvio and Gong intervened, challenging them to another duel. They were also defeated; fortunately Yuya and Shay arrived to challenge the sisters to another duel. Yuya treats the sisters to a bout of "dueltaining", and along with Shay, consign the sisters to defeat. Their mission was taken over by the Obelisk Force, who had been sent over as backup. When the Obelisk Force summoned "Chaos Ancient Gear Giant", it caused shockwaves that caused debris to fall. Shay pushed Saya out of the way and was badly injured by the shockwaves. Kite then returned, joining the duel against the Obelisk Force and driving them away. This led to one final showdown between Yuya and Aster, with Kite leading the rest of the Resistance to safety.
Aster fell to defeat, and chose to defect from Duel Academy. The Tyler sisters had also defected by then, and together with the Resistance, they forced Mamoru to surrender as well. Aster's forces became volunteers that helped to rebuild the Xyz Dimension after causing much of its devastation, and later offered to transport Yuya, Gong, Sylvio and Kite to the Fusion Dimension using their Interdimensional Travel Device located at Duel Academy's former Heartland base. Kite left to pursue Dennis McField while the other three Lancers reunited with Zuzu. Zuzu told Yuya that she found his father, and hurried to the port with the Lancers, but Yusho's ship had already set sail. Celina appeared, and found the Lancers another ship to board, this one captained by Cutter. During their journey, Celina betrayed the Lancers by capturing Zuzu and taking her on board Duel Academy's helicopters, while the ship's crew tied up Sylvio and Gong, forcing Yuya to duel Cutter. Fortunately, the other Lancers (Declan, Riley, Sora, Crow and Moon Shadow) arrived on a speedboat; they saved Yuya, Gong and Sylvio while Sora engaged Cutter for the rest of the duel.
During the Duel Academy arc, the reason for invading the Xyz Dimension and sealing their populace into cards was revealed: the cards' life energy was required in order to power up a machine called the ARC-V, which ultimately fulfilled the end goal of the Arc Project - the fusion of the Four Dimensions back to their original state as a United World. Declan and Yusho confronted Leo over his plans, and when Leo revealed the four girls, each in separate capsules, he also revealed that the girls were reincarnations of his daughter, Ray Akaba, which the fusion of the Dimensions under ARC-V would also bring back. Yusho then deduced that, by capturing the girls, Leo also took away the safety measure that prevented Z-ARC's counterparts from seeking each other and responding to Z-ARC's will to become whole again, because it was Ray's will to keep Z-ARC fragmented, by ensuring Ray's fragments would stay close to Z-ARC's fragments. Despite all this, Leo pressed on with his plans, revealing that the ARC-V was already being powered up during his duel against Yuya and Declan.
Eventually, the ARC-V reached 50% completion, causing the girls to faint inside their capsules. Leo rushed the revival process by transferring Lulu, Rin and Celina before the ARC-V reached a sufficient energy level, and when the inevitable - Z-ARC's revival - happened, Ray took the form of a bodiless spirit. At the same time, the dimensions were beginning to merge, and people that had been sealed into cards were being freed. Z-ARC accepted the challenges of duelists from all sides of the Interdimensional War - Duel Academy personnel (Sora Perse and Aster Phoenix), members of the Resistance (Kite Tenjo and Shay Obsidian), as well as the remaining Lancers and their allies (Gong Strong, Jack Atlas, Sylvio Sawatari and Crow Hogan). Finally, the Akaba family confronted Z-ARC personally: Leo, Declan and finally Ray (possessing Riley's body). After Z-ARC's defeat, the four dimensions began to split again, but Riley ejected Ray's spirit from her body, removed Z-ARC's spirit from Yuya's body and sealed Z-ARC's spirit within herself, preventing Z-ARC's revival and finally ending the Interdimensional War.