Maybe a new character could be the main antagonist. A powerful and mysterious being that Luigi stumbles upon during his escape. This character might have some vendetta against the Mario brothers or just be generally evil and wants to stop Luigi's journey for its own malicious reasons.
Another possibility is that the main antagonist is a corrupted version of one of Luigi's friends. Maybe a spell was cast on them, and they now try to stop Luigi from achieving his goals while he's running away. This would add an interesting layer of conflict as Luigi has to face someone he once trusted.
Well, perhaps Luigi runs away because he's tired of living in Mario's shadow. He might decide to explore new lands on his own, meet new characters, and have adventures that are just about him, not always being the sidekick.
Maybe an organization that specializes in using the Sharrigan for malicious purposes. They don't want Naruto to expose their secrets, so they send their Sharrigan - users to hunt him down. This organization could be made up of power - hungry individuals who will stop at nothing to achieve their goals.
Wario could also serve as an antagonist. He might be envious of Luigi's new married life and try to steal their treasures or disrupt their happiness. Maybe he spreads false rumors about Luigi in the Mushroom Kingdom just to create chaos in their lives.
Bowser could be the main antagonist. He might see Luigi's transformation as an opportunity to mess with Mario and the Mushroom Kingdom. He could try to use Luigi's new form to his advantage, perhaps by trying to make Luigi a spy or by using his new identity to cause chaos among the kingdom's residents.
Another option could be an evil version of Princess Peach. She could be possessed by some dark force. This would be a very interesting antagonist as Mario and Luigi would be hesitant to fight her at first because of their loyalty to the real Peach. But as she causes more and more chaos, they'd have to find a way to save her and the kingdom without harming her.
Obviously, Percy would be the main character. But there could also be his friends who might be trying to find him after he runs away. For example, Annabeth could be a major character in the story as she would be worried about Percy and use her intelligence to track him down.
There could be a group of purist wizards who believe that magical animals should not be put on display for non - wizards to see. They constantly try to disrupt the zoo's operations, causing trouble for Harry. Harry would need to fight for the right of his zoo to exist and educate these purist wizards about the importance of co - existence between wizards, non - wizards, and magical animals.
It could be Orochimaru. He has always been interested in power and Naruto's unique abilities. With Naruto sealed away, Orochimaru might see it as a chance to steal whatever power Naruto had or use his absence to further his own evil plans in the ninja world.
A corrupt leader from a political - based crossover world might be the main antagonist. He views Naruto as a threat to his power, especially with the mystery of his seal. So, he tries to either keep Naruto sealed away permanently or use the situation to gain more control over his own people by creating fear around Naruto's presence in their world.
The main antagonist could be some dark wizards who want to use the dragon for their evil purposes. They might be after the dragon's scales, which are valuable in making powerful dark magic items, or its fire, which can be harnessed for destruction. They would oppose Hermione's attempt to move the dragon away as it would thwart their plans.