Perhaps it's a powerful wizard. In this fanfiction world, magic exists and the wizard sees the bird kid as a threat or a valuable asset. The wizard uses dark magic to trap the bird kid in an enchanted cage, and the bird kid has to find a way to break the magic spell to escape.
There's also the chance that the main villain is another bird kid who has turned bad. This bird kid is jealous of the protagonist's abilities or has been corrupted by some outside influence. They use their knowledge of the bird kid world to set up a trap for the innocent bird kid.
Well, it could be about a bird kid who is trapped in a cage made by some evil force. Maybe this force wants to use the bird kid's special abilities for their own bad purposes. The bird kid might have wings that can do extraordinary things like fly super fast or create strong winds.
Maybe a group of rogue nymphs who are angry at how the demigods have been treating the natural world. They trap Percy as a warning to the other demigods, and he has to negotiate with them and find a way to make amends for the actions of his kind.
Maybe the Riddler. He could set up a series of elaborate riddles that not only challenge Batman but also the curious kid OC. The kid's fresh perspective might actually help Batman solve the riddles faster and catch the Riddler before he executes his grand plan.
Perhaps a ninja who has a grudge against Naruto because he once ate all the ramen at a festival, leaving none for the ninja. So this ninja decides to target Ichiraku Ramen and tries to put a curse on the ramen that would make anyone who eats it sick. Naruto has to figure out how to break the curse and stop the ninja.
Thanos could also be a good option. Imagine Bella's planet holds one of the Infinity Stones that Thanos needs. He would stop at nothing to get it, and Bella and the Avengers would have to join forces to protect it. Thanos' brute strength and strategic mind would pose a huge challenge for them.
A powerful sorcerer could be the main villain. This sorcerer has the ability to control minds and is using it to turn some of the Huntsmen and Huntresses against their comrades. He aims to take over Remnant and rule with an iron fist.
A secret society that has been observing the Avatar from the shadows could be the main villain. They believe that Aang's power is too great and unpredictable, so they use some ancient and powerful artifacts to make him disappear. The heroes would then have to figure out how this society operates and find a way to reverse the spell or device that made Aang vanish.
Plankton could be a great main villain in a Spongebob vampire fanfiction. He could team up with a group of vampire - like creatures from the deep sea. He wants to use their powers to finally take over the Krusty Krab. He might offer them all the Krabby Patties they can eat if they help him get rid of Spongebob and Mr. Krabs.
The main villain could be an ancient Titan who was imprisoned long ago but has now found a way to break free. This Titan could be seeking revenge on the gods and demigods alike, and Percy and his friends would have to stop him before he destroys the world as they know it.
It could be Orochimaru. He's always interested in new forms of power and experimentation. He might see Wolverine as an interesting specimen to study and try to extract his healing factor or adamantium for his own purposes. This would put him in direct conflict with both Wolverine and Naruto, who would naturally oppose Orochimaru's evil plans.