In this fanfiction, it could be that Percy is forced to work for Kronos due to a prophecy. Kronos sees Percy as a valuable asset because of his powers. Percy, while working for Kronos, tries to change Kronos from within. He uses his charm and intelligence to influence Kronos' decisions, trying to steer him away from destruction. But he also faces a lot of internal conflict as he is going against his own principles and the trust of his friends.
One possible plot could be Percy starting off reluctantly working for Kronos. Maybe Kronos has some sort of leverage over Percy, like threatening his friends or family. Percy then has to play a double - agent role, secretly trying to undermine Kronos' plans while appearing to be loyal. He could gather information about Kronos' forces and weaknesses and pass it on to the good guys.
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.
One possible plot could be that Percy discovers his true relation to Kronos early on. This revelation could cause a great deal of inner turmoil as he has to come to terms with being related to the main villain. He might then struggle with whether to side with his friends or his new - found brother, creating a complex moral dilemma.
One possibility is that Kronos captures Percy to steal his powers. Percy, being a powerful demigod, has abilities that Kronos desires for his own evil plans. While captured, Percy may discover some secrets about Kronos' past that could be used against him. He has to use his wits and any small resources he has in the prison to outsmart Kronos and break free.
In many fanfictions, Percy might use his water powers in a unique way. Maybe he combines his control over water with his sword fighting skills. He could create a giant water vortex to disorient Kronos and then strike with Riptide while Kronos is off - balance.
The plot could involve her on a quest. Maybe she's searching for a way to break the cycle of Kronos' evil. She might team up with Percy Jackson and other characters. They could face various monsters and challenges along the way. And she could be constantly battling her own inner demons related to her father's nature, like a tendency towards power - hunger that she has to overcome.
One possible plot could be Percy's journey to discover his true identity as the son of Kronos and Rhea. He might face challenges from the other gods who fear his power. For example, Zeus could try to stop him from fully realizing his potential. Percy would also have to deal with his own internal struggle. He grew up believing he was Poseidon's son, so this new revelation would shake his world. He could start a quest to find out more about his parents' relationship and what it means for him in the grand scheme of the mythological world.
The plot could start with Percy being somehow influenced by Kronos, maybe through a dream or a cursed object. Then he slowly starts to act in ways that are out of character for him. He might begin to gather followers who are also attracted to the power that Kronos represents. Eventually, he could lead an uprising against the gods, believing that he can create a new world order under Kronos's ideology.
Well, one possible plot could be Percy having to hide his relation to Kronos while still fighting against the Titans. He might struggle with the internal conflict of having a connection to such an evil entity as Kronos while trying to protect his friends at Camp Half - Blood.
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.
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.