It could be a powerful mage who wants to use Percy's demigod powers for his own evil plans. This mage might be jealous of Percy's unique abilities and try to control him.
Another option could be a group of Forsworn who have somehow discovered Percy's connection to the gods. They might try to capture him and sacrifice him to their dark gods in the hopes of getting more power. Percy would then have to use his skills from both his demigod life and what he's learned in Skyrim to fight against them.
It could be a character who is jealous of the power that could come from combining the two worlds. Maybe a rogue demigod who wants to use Jessie's knowledge of her world's technology and the magic of the Percy Jackson world to rule over both. This character might start causing problems by stealing important artifacts from both worlds to try and build a device that would give them ultimate power.
Perhaps a rogue demigod who has made a deal with a speed - based meta - human villain from the Flash's world. Together, they plan to take over both the magical realm and Central City. The demigod could use his powers in combination with the meta - human's technology to create some really tough challenges for Percy and the Flash.
A possible main antagonist could be a new character created specifically for this fanfiction. A scientist who has somehow managed to combine Greek magic with Hydra technology. This character could be creating powerful hybrid creatures that are causing havoc in both Percy's world and the Marvel universe. Percy and Black Widow would need to put aside their differences and work together to stop this mad scientist.
A 'Percy Jackson Skyrim Crossover Fanfiction' could involve Percy getting lost in Skyrim. He would have to adapt to the different magic system there. His sword - fighting skills and his powers over water could make him a very unique character in the Skyrim world. For example, he could use water to put out dragon fire or find hidden underwater caves that are full of treasures and ancient Skyrim secrets.
It could be an old enemy of the gods who has a vendetta against both Camp Half - Blood and Camp Jupiter. This antagonist might see Percy and Reyna as threats because of their combined power and influence among the demigods. For example, a powerful Titan who escaped from Tartarus and wants to use the chaos between the two camps to his advantage.
A powerful and corrupted nymph could be a great antagonist. She could be jealous of Piper's charm - speaking abilities and Percy's status as a hero. So, she uses her nature - based powers to create all kinds of obstacles for them. For example, she might cause floods in areas they need to cross or make the plants come alive to attack them.
Definitely Yugi and Percy. Yugi is the heart of the Yugioh series with his connection to the Millennium Puzzle and his dueling skills. Percy, on the other hand, is the hero of the Percy Jackson series, a demigod with his own set of powers. They would be the ones to bring the two worlds together and lead their respective groups in any adventure or conflict.
A powerful demigod who has been corrupted by the idea of primordial power could be the main antagonist. They might believe that by allying with a primordial or obtaining their power, they can become greater than the gods. This demigod would then oppose Percy, who stands for the protection of the current order.
An ancient and forgotten god who has been awakened. This god could be angry at the modern demigods for ignoring the old ways and decides to send assassins after Percy as a warning to the rest. They might want to bring back the old order where gods were feared and worshiped more and see Percy as a symbol of the new, more independent demigods.
Perhaps an ancient and dark deity who has been awakened due to some event related to Percy's exile. This deity wants to bring chaos to the world of gods and demigods, and Percy, even in exile, is the only one who can stop it. The deity would use all kinds of dark magic and minions to oppose Percy and his friends.