Perhaps a group of rogue duelists who have formed a cult dedicated to the idea of a single all - powerful dimension. They believe that by destroying all other dimensions, they can create a utopia in their own. They start the dimension war by attacking other dimensions and stealing their most powerful cards and resources, and they are willing to do whatever it takes to achieve their goal, making them a formidable and relentless antagonist.
A powerful and corrupted duelist from a forgotten dimension could be the main antagonist. This duelist might have discovered a way to harness the power of the dimensional rifts for his own evil purposes. He could be using this power to create chaos and destruction across all the dimensions, and only the combined efforts of the heroes from different dimensions can stop him.
A group of rogue ninja from the other dimension could also serve as the main antagonists. They might be jealous of Naruto's power from his original dimension and want to steal it for themselves. They could be led by a charismatic and devious leader who has a personal vendetta against Naruto for some reason, like he believes Naruto will disrupt their way of life in the dimension.
It could be an alternate version of Orochimaru. Maybe in this new dimension, he has achieved ultimate power and is using it to control the different ninja villages.
Perhaps a group of rogue time - traveling wizards. They come from a future in this dimension where the wizarding world has been destroyed, and they believe that changing the past (even if it means causing chaos) is the only way to save their future. They see Harry as a threat to their plans because he has a natural inclination to preserve the present order.
Maybe it's a corrupted version of one of the gods from Percy's world who has gained even more power in this new dimension. They could be trying to spread chaos and destruction, and Percy has to stop them. This antagonist would know Percy's weaknesses from their time in the original world, which would make the conflict more intense.
A new character could also be introduced as the main protagonist. This character might start as an unknown in the 'Yugioh Zexal' universe but gradually gain power and importance as they journey across the dimensions. They could have a special connection to the different dimensions that sets them apart from the existing characters.
It could be a corrupted version of one of the Fairy Tail members from the other dimension. For example, an evil Natsu who uses his fire magic for destruction and domination. The real Natsu would have to face his own dark self and find a way to defeat him without losing his own identity.
It could be a rogue teacher at Duel Academy who has his own dark motives. He might be secretly researching dangerous dueling techniques and using students as guinea pigs for his experiments.
It could be Yuya Sakaki. Since he is a central character in the Yugioh Arc V series, he might also play a major role in the fanfiction related to the Ritual Dimension. He could be exploring the Ritual Dimension and facing new challenges.
In a crossover with the Pokémon universe, an evil Team Rocket - like organization could be the main antagonist. They might try to steal powerful Duel Monsters cards and use them for their own evil purposes. They could see the power of the cards as a way to take over both the Pokémon and Yugioh worlds. They might even try to combine the powers of Pokémon and Duel Monsters in some diabolical plan.
One idea could be that the characters from different dimensions team up to fight a common enemy that threatens all dimensions. For example, Yugi and his friends could join forces with counterparts from a dark dimension who have their own unique cards and strategies. This would lead to some really cool duels and character interactions.