One possible plotline could be Harry discovers a secret passage that leads out of Hogwarts in a completely unexpected place, like inside the Room of Requirement. Another might be that he has to use a new spell he learned from an old book to break through the magical barriers around Hogwarts while escaping.
Harry Potter himself is obviously a main character. He's usually the one trying to escape. His friends Hermione Granger and Ron Weasley are often involved too, as they would never leave Harry alone in such a situation.
They would probably be shocked at first. I mean, Hogwarts reading fanfiction? It's a strange concept. But then they might be really curious about what Hogwarts is reading. They could try to get their hands on the same fanfiction to see what all the fuss is about.
One possible reason could be that the author of the fanfiction wants to explore a different storyline. Maybe they want to show Harry facing challenges outside the familiar Hogwarts environment, like in the wizarding world at large or in Muggle society.
He might lose the support system he had at Hogwarts. His friends like Ron and Hermione would be separated from him, which could lead to changes in their relationships. They might have to find new ways to communicate and support each other.
In the fanfiction world, Harry might be the heir to Hogwarts if there was some sort of magical pact made generations ago. For example, perhaps one of his ancestors had a special role in the creation or protection of Hogwarts, and this role was passed down through the family. It could also be that his unique magical abilities, like his ability to resist Voldemort's attacks from a young age, are signs of a deeper connection to Hogwarts itself. This connection could be what designates him as the heir in the fanfiction's plot.
One possible reason could be that he was under the influence of a powerful dark magic or a curse that made him lose control. Another reason might be that he was tricked into believing Hogwarts was a threat to the wizarding world in some extreme way. Maybe a powerful enemy manipulated him to think that destroying Hogwarts was the only way to save everyone.
He could use his Invisibility Cloak. The Avengers might not be able to detect it with their technology. Then he could find a way to apparate out if he's far enough from any anti - apparition charms.
Yes, in many fanfictions, Harry Potter can have special interactions with Hogwarts, like it being a sentient entity he can communicate with. It adds an interesting twist to the story.