The main villain could be a power - hungry Atlantean sorcerer who wants to use the power of Atlantis to rule both the underwater world and the surface. He might see Percy as a threat to his plans and try to eliminate him.
Maybe it's an ancient sea monster that has been awakened from its slumber beneath Atlantis. This monster is angry at the world for disturbing its peace and decides to take revenge by destroying Atlantis first and then the rest of the world. Percy has to stop it, but it's extremely powerful and has some dark magic on its side. The monster could have some connection to the history of Atlantis that makes it even more dangerous.
The Titans could still be a major threat. Even though they were mostly defeated in the original series, some of their followers might see Percy's new role in Atlantis as a threat to their plans for chaos. They could try to undermine Percy's position in Atlantis and use the underwater city as a base for a new uprising.
It could be a power - hungry Atlantean noble who wants to rule not just Atlantis but also the surface world. He sees Percy as a threat to his plans and tries to stop him at every turn.
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.
An ancient and powerful Titaness who was banished long ago could return. She is angry at both the Greek gods and the current Titans. So she decides to use Percy as a pawn to start a war between the two groups so she can emerge victorious and rule over all.
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 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 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.
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.
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 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.