A group of rogue demigods could be the main antagonists. They believe that the appearance of the angel of God is a sign that the old order is about to change and they want to use this opportunity to take over. They oppose Percy because he is seen as the one who will work with the angel to maintain the balance. They would use their demigod abilities in unethical ways to try and achieve their goal of domination.
Perhaps a powerful sorcerer who has somehow managed to gain control over some of the angelic powers and wants to use them to rule the world of demigods. He could be jealous of Percy's connection to the angel of God and see him as a threat to his plans. This sorcerer would use dark magic combined with the misused angelic powers to create all kinds of obstacles for Percy and his friends.
One possible main antagonist could be Cronus, an Elder God. He has a history of trying to overthrow the Olympians and could be plotting a comeback in the fanfiction. He could be using his powers to corrupt demigods and turn them against each other, all in an effort to regain his former glory and power over the world.
Maybe it could be a group of dark sorcerers. They are jealous of Percy's newfound powers as the God of the Sun and they want to use his power for their own evil purposes. They try to trap Percy and steal his powers by using dark magic and illusions.
It could be a new and unknown deity who is jealous of Percy's sudden ascension to the status of God of Elements. This deity might be able to manipulate the dark aspects of the elements and use them to create havoc and try to defeat Percy. For example, the deity could create poisonous miasmas using the water element or uncontrollable infernos with the fire element. He would constantly be one step ahead of Percy, making him a very difficult antagonist to deal with.
It could be an ancient and powerful Titan who was once in charge of fate but was overthrown. Now he wants to regain his power over fate and sees Percy as a threat. He might try to manipulate Percy into making bad decisions regarding fate.
A powerful dark wizard or sorcerer from a different realm could be the main antagonist. The eclipse could have opened a portal to their realm, and they see the world of Percy Jackson as a new place to conquer. They would use their dark magic against Percy and his friends, and Percy, as the God of Eclipse, would have to use his unique powers to stop them.
It could be a new, dark demigod who has been corrupted by dark magic. This demigod might envy Percy's relationship with the gods and the God of Thunder in particular. He or she could be gathering an army of monsters and using dark powers to try and take over the world of the demigods and gods alike. They would be a formidable foe as they understand the ways of demigods but also have access to dark powers that are not easily countered.
A powerful Titan who was once in charge of storms and wants his power back. He sees Percy as a threat and tries to stop him at every turn.
It could be a jealous demigod. Maybe someone who has always been in Percy's shadow and decides to frame him for betraying the gods in order to get rid of him and gain more power and recognition among the demigod community.
It could be a dark demigod who is also seeking the power of the first god but for evil purposes. This demigod might be jealous of Percy's connection to the first god and tries to stop him at every turn.
The main antagonist could be a cult that worships the dark god of lust. They might be trying to bring about the full power of the dark god by using Percy as a sacrifice or a vessel. They would be constantly opposing Percy and his friends, trying to stop them from thwarting their evil plans.