Perhaps there are some traitors from the other side. These characters, seeing Kronos' power and potential for victory, switch sides and help him in the war. They might provide valuable information about the enemy's defenses and plans.
Some of Kronos' minions, like the monsters he commands, could be antagonists. For instance, the dracaenae. They are always eager to prove themselves to Kronos and might see Percy as competition within Kronos' ranks. They could constantly try to undermine Percy's position and cause trouble for him.
In the 'kronos wins the war fanfiction', it might be that Kronos discovers a powerful weapon or magic. This newfound power allows him to overpower his enemies one by one. He could also be very cunning in manipulating the internal conflicts of his opponents, which in the end helps him win the war.
The other Titans could be main antagonists. For example, Hyperion who is known for his great strength and his desire for destruction. He might not fully trust Percy and constantly try to undermine him in Kronos' eyes. Another could be Atlas, who is already a major foe in the Percy Jackson series. He might see Percy as a threat to his own plans within Kronos' regime.
Maybe there are some original characters created by the fanfiction author. These characters could have their own unique abilities and backstories. They might be the ones who tip the scales in Percy's favor, for instance, by having a special power that weakens Kronos just before Percy makes the final blow.
If Kronos were to win in a Percy Jackson fanfiction, it would be a cataclysmic event. Kronos represents the old, chaotic order. His victory would mean the collapse of the current pantheon - based system. The gods' domains would be up for grabs, leading to widespread conflict among the Titans and other powerful beings. Percy and his allies would have failed in their quest to protect the world. The very fabric of the Percy Jackson universe, with its themes of friendship, heroism, and the fight against tyranny, would be shredded. It would be a very different and much darker world than the one we see in the original series.
Annabeth is often a popular character. In fanfiction, she might play a crucial role in helping Percy deal with his complex identity as the son of Kronos. Grover could also be popular as he's Percy's loyal friend and could be there to support Percy through his struggles related to his new - found heritage.
Luke could also be a prominent character. Since he has a complex relationship with Kronos in the original story, in fanfiction he could play a role in either helping or hindering fem Percy's efforts against Kronos. Nico di Angelo is another possibility. His powers over the dead could be useful in a fight against Kronos, and he might team up with fem Percy for that reason.
Obviously, Percy Jackson is one of the main characters. He is the demigod hero with his own set of powers and a strong sense of justice. And then there's Fem Kronos. She is a female version of the powerful Titan Kronos. Her character might have different motives and ways of operating compared to the male Kronos we know from the original myths. There could also be other characters like Annabeth, Percy's friend and strategic partner, who might play a role in the fanfiction, either helping Percy against Fem Kronos or getting caught in the middle of their conflict.
Obviously, Percy and Kronos are the main ones. Percy, the demigod son of Poseidon, is likely to be the hero of the story. Kronos, the powerful Titan, is the antagonist that Percy has to face.
Obviously, Percy is the central character. As the heir of Kronos, he is the focus of the story. His friends like Annabeth are also important characters. Annabeth often serves as Percy's moral compass, trying to keep him from fully succumbing to the dark influence of his new heritage. Grover might also be there, providing his usual support and comical relief.