There might be a vengeful god or goddess who is angry at Percy for some reason. They could send minions or use their own powers to break Percy's bones as a form of punishment. This would create a really interesting dynamic as Percy would have to figure out how to either make amends or fight back against a much more powerful being.
It could be a new, powerful monster. Maybe a giant with the ability to shatter bones just by looking at a person. This monster could be targeting Percy specifically because of his reputation as a hero among the demigods.
Perhaps an evil demigod who has a grudge against Percy. This demigod could use some dark magic to cause Percy's bones to break and then try to take over his role at Camp Half - Blood or gain some sort of power that Percy was supposed to have. They would be a really sneaky villain, using their knowledge of the demigod world against Percy.
One possible plotline could be Percy having to deal with broken bones during a quest. Maybe he gets injured while fighting a monster and has to find a way to continue the mission with his injury. Another could be that his broken bones are the result of a prank gone wrong by one of the other campers, leading to some comical and tense situations at Camp Half - Blood.
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.
Luke Castellan can be considered an excellent villain in fanfiction too. His journey from a disillusioned demigod to a servant of Kronos is full of angst and betrayal. He has a deep understanding of the demigod world, which he uses against his former friends. His complex character, with his own reasons for turning bad, adds a lot of depth to the stories where he is the main villain.
Perhaps it could be a centaur who was once a great guardian of the forest but has been broken by the encroachment of dark forces. Or it could be a minor god who was supposed to protect a certain aspect of the world but has failed and is now in a broken state. There are many possibilities within the rich lore of Percy Jackson.
Maybe a group of rogue demigods who have decided to take over the Hollow for their own purposes. They could be using the resources of the Hollow in a wrong way, like trying to extract its magic to make themselves more powerful. They would be a formidable foe as they have demigod abilities.
Perhaps a minor god who is jealous of the attention the major gods get. This god decides to cause trouble at the zoo. He could be the one responsible for making the magical creatures in the zoo act up. He would try to stop Percy from uncovering his plans and restoring order at the zoo. He might have some strange powers related to the natural elements found in a zoo, like the ability to make plants grow wildly to entangle Percy or make the water in the ponds turn into quicksand - like substances.
Kronos could make a comeback. Even though he was defeated before, he could find a way to return in a more powerful and vengeful form. He could be the mastermind behind the apocalypse, seeking to finally destroy the gods and take over the world once and for all.
Maybe a new type of monster that is created or awakened during the eclipse. This monster could be immune to most of the demigods' powers during the eclipse, making it a very difficult foe. It could have the ability to manipulate shadows, which are stronger during the eclipse, and use them to its advantage in battles against Percy and his friends.
It could be Kronos again, but in a more powerful and resurrected form. He might have found a way to come back even stronger after his previous defeat and now has a new plan to take over the world of gods and demigods.
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.