Perhaps the fanfiction has a plot where Hogwarts is no longer the safe haven it used to be for Harry. There could be a new regime or a powerful dark force at work that the fanfic writer has created, and Harry, in order to protect himself or seek a solution away from the source of the problem, decides to leave Hogwarts.
Maybe the fanfiction portrays some really dark and disturbing events that make Harry feel he can't stay at Hogwarts anymore. For example, if it involves his friends being seriously harmed in the fictional story in a way that he can't bear to be associated with the place where it all seems to be happening.
It could be a new dark wizard or witch who has infiltrated Hogwarts in the fanfiction. This character might be causing all sorts of trouble like spreading dark magic among the students or causing unrest between different houses.
One reason could be that she might be on a secret mission. In some fanfictions, she could be trying to find a powerful magical artifact outside the walls of Hogwarts to save the wizarding world from a new dark threat. She might believe that she can't achieve this while staying within the school's confines.
It could also be due to personal reasons related to his growth and self - discovery. The events of the Triwizard Tournament might make him realize that he needs to find his own path outside of Hogwarts for a while. He might feel that the school can't offer him the answers or the experiences he needs at that moment to become stronger and more independent.
Maybe she leaves because of a conflict. It could be with a teacher who doesn't support her unorthodox ways of learning or a fellow student who makes Hogwarts an unpleasant place for her. In fanfiction, there could be a lot of creative interpretations of such conflicts.
One possible reason could be that she's frustrated with the school's bureaucracy. For example, if she constantly faces obstacles in getting approval for new study groups or advanced classes. Another reason might be a personal quest. Maybe she discovers a hidden mystery outside of Hogwarts that she can't explore while being a student there.
In some fanfictions, there could be a change in the Hogwarts admission policy. Maybe they found some supposed flaw in Harry's magical abilities or his background that led to his admission being revoked at the last minute, so he didn't arrive at Hogwarts. Also, it's possible that some other powerful magic was at work. A powerful wizard or witch could have cast a spell on Harry that made him forget about Hogwarts or made it so that he couldn't physically reach the school.
One reason could be that he doesn't like others taking creative liberties with his story. He might feel that it's his story and only the original version should be the 'true' one.
One possible plot could be that Harry leaves Hogwarts to hunt down the remaining Death Eaters on his own. He might feel that he can't put his friends in danger anymore and takes it upon himself to rid the wizarding world of the last remnants of Voldemort's followers.
One reason could be that he's being hidden by some powerful magic from a group that wants to use him for dark purposes. Maybe there are dark wizards who know of his future importance and want to either kill or control him, so a good wizard has made him disappear.
One reason could be to search for a powerful magical artifact outside of Hogwarts that they believe is crucial for defeating a new dark threat. In fanfiction, they might feel that Hogwarts has become too dangerous or restricted in terms of resources for their mission.