Well, one possibility could be that Percy is framed for a crime he didn't commit. Maybe some powerful enemy uses magic or trickery to make it seem like he's violated a major demigod law. So, he's sent to a special prison for demigods. Inside, he has to deal with all sorts of other dangerous inmates, some of whom might be old enemies or just generally bad - tempered demigods. He'd probably try to find a way to prove his innocence and escape while also having to survive the various challenges within the prison.
There could be an ancient and evil force that has infiltrated the demigod world. This force uses Percy as a scapegoat and arranges for him to be sent to prison. It wants to cause chaos and destruction within the demigod community. It manipulates the situation from the shadows, and Percy has to figure out its identity and motives while in prison in order to stop it.
Percy going to Ilvermorny would be a wild ride. First, he'd be amazed by the castle itself. The four houses would be a new concept for him. He might be sorted into a house based on his heroic nature, like Thunderbird perhaps. He'd introduce the idea of Greek gods to the students there, which would cause quite a stir. And his relationship with Annabeth would be put to the test as they are separated by different magical institutions.
He might meet some talented witches and wizards. Maybe there would be a student who is an expert in magical beasts and they could share stories about their encounters with strange creatures.
Percy might meet an old enemy who has somehow been resurrected or changed in the future. This enemy could be more powerful and have a new plan to take over the world or destroy the demigods. Or he could meet a group of time - traveling demigods from an even further future who are trying to fix something in Percy's future that has gone wrong.
Percy might run into Loki. Loki is known for his trickery. He could either befriend Percy for his own devious plans or try to deceive him. Percy, being used to dealing with tricky situations in his own world, would have to be on his guard against Loki's schemes.
In this fanfiction scenario, Percy's adaptation to Hogwarts would be a complex process. He'd first have to deal with the cultural shock of a new magical world. The Hogwarts houses would be different from the cabins at Camp Half - Blood. He'd need to figure out which house he belongs in. His skills with a sword might not be as useful as in his own world, but he could learn to use magic to enhance his combat abilities. Also, he'd have to make new friends and enemies, and learn how to navigate the social politics of Hogwarts while still holding on to his own identity as a demigod.
Some of the more traditional and rule - following demigod groups at Camp Half - Blood could be against him. They believe in following the established ways and Percy's rogue behavior goes against that. They might see him as a troublemaker and try to bring him back to the 'right' path.
In fanfiction, if Percy Jackson goes to highschool, he might face challenges like hiding his demigod powers from his classmates. He could also encounter new mythical creatures that are drawn to the school environment.