I really like the fanfic 'Villainous Intent'. It focuses on a group of villains in the Percy Jackson universe coming together to form a new, more powerful threat. The author does a great job of showing their motives and how they interact with each other, which makes it a very engaging read. It's full of action and plot twists that keep you on the edge of your seat.
Well, good character development of the villains is key. In a 'Percy Jackson Villain Fanfic', if the author can make the villain more than just a one - dimensional evil character, like showing their vulnerabilities or complex motives, it becomes very engaging. Also, an exciting plot that involves the villains in new and unexpected ways, such as teaming up with unlikely allies or having a different end goal than just causing chaos, can make the fanfic really stand out.
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.
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.
It could be Kronos from the Percy Jackson universe. He could somehow find a way to cross over to Daenerys' world and try to take over. He would see her dragons as a great source of power and want to control them for his own evil purposes. Daenerys and Percy would have to put aside their differences and combine their powers to stop Kronos.
It could be a villain who wants to merge the Greek and Egyptian mythologies in a chaotic way. Maybe a powerful sorcerer who thinks that by combining the powers of the two worlds without any order, he can become the ultimate ruler.
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.
Loki could be a great villain. He's known for his trickery in Norse mythology. He could manipulate events to set Magnus and Percy against each other. Maybe he wants to cause chaos between the Norse and Greek worlds for his own amusement or to gain more power.
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.
First, you need to understand the existing villains in the Percy Jackson universe. Know their motives, their powers, and their backstories. For example, if you're writing about Kronos, you should know about his desire to overthrow the Olympians. Then, create a unique plot. Maybe give the villain a different goal or a new way to achieve their existing goals. For instance, instead of Kronos just using Luke as a pawn, he could have an additional secret weapon.