Perhaps there could be a plot where Percy gets trapped in Medusa's lair in a different way. Instead of just a simple exploration gone wrong, he could be lured there by a false prophecy. And Medusa, instead of immediately attacking, toys with him, leading to a series of mind - games and challenges that Percy has to overcome to escape.
A great plot might involve Medusa having a change of heart. For example, instead of being purely evil, she could be forced into her actions by some greater power. Percy then discovers this and has to decide whether to still fight her or help her. In a fanfic, this could add a whole new layer of moral complexity to their relationship. It could also lead to an alliance between them against a common enemy, which would be very different from the traditional view of their encounter.
In a fanfic, perhaps Percy and his friends accidentally stumble upon Medusa's lair while on a quest. But instead of immediately attacking, Medusa offers them a deal. She says she will give them a valuable clue to complete their quest if they help her get revenge on one of the minor gods who wronged her in the past. Percy and his friends then have to decide whether to trust Medusa or not.
One interesting plot could be Percy having to face off against Medusa's other children in a battle of wits and strength. Maybe they are out to prove themselves as worthy as Percy, who has the fame of being Poseidon's son. Another could be Percy having to deal with the stigma of being 'Son of Medusa' in a world that fears her so much. He might have to constantly prove he's not a monster like his 'mother' is perceived.
One interesting plot is Percy being summoned by a time - traveling device. He is brought to a future where the Greek gods are forgotten and the world is in chaos due to the lack of their influence. Percy has to find a way to bring back the knowledge of the gods and restore order, all while dealing with the strange new technology and a society that has lost its moral compass.
One possible plot could be that in the fanfic, Jason is jealous of Percy's natural leadership skills. Percy always seems to know what to do in a crisis, and the other demigods look up to him. Jason, on the other hand, feels like he has to constantly prove himself. So, he starts trying to outdo Percy in every mission, which leads to some tense and exciting situations. For example, they might both be trying to solve a mystery at Camp Half - Blood, and Jason's jealousy causes him to take unnecessary risks just to show he's better than Percy.
Sometimes, the plot revolves around Percy and the members of his harem going on adventures together. They could be exploring new and mysterious places, and during these adventures, their relationships develop and they face challenges as a group. In some 'percy x harem fanfic', there are also plots where Percy has to deal with jealousy and rivalry among the harem members, which creates a lot of drama and interesting relationship dynamics.
One interesting plot could be Percy having to face a new and powerful monster that is immune to water, which is his usual strength. It creates a whole new level of challenge for him.
One possible plot could be Percy's struggle for survival in a harsh and unforgiving environment. Maybe he has to find food and water while fending off dangerous creatures. Another plot could involve Percy trying to figure out who left him for dead and seeking revenge.
One interesting plot could be Percy's internal struggle with his new identity as the child of Kronos. He might battle against the dark urges that come with his heritage while trying to stay true to his friends at Camp Half - Blood. Another plot could involve Percy facing off against the other demigods who see him as a threat due to his relation to Kronos.
One interesting plot could be Shirou and Medusa teaming up to face a powerful common enemy. Maybe an ancient evil that threatens the world they are in. They would combine their unique abilities, with Shirou's projection magic and Medusa's powerful combat skills and snake - based powers.
A really unique plot could be that Poseidon and Medusa's love is a way to bring about change in the world of the gods. Their union could be seen as a symbol of breaking free from the traditional norms. Medusa, with her unique powers, and Poseidon, with his vast influence over the seas, could team up to create a new era. However, they face many obstacles like the jealousy of other gods and the strict rules of the divine hierarchy.