It could also be due to a new, strict headmaster who has a different view on Harry. Maybe this headmaster believes that Harry is a bad influence because of his association with dangerous situations. For instance, if there are a series of attacks at Hogwarts and the headmaster blames Harry's presence for attracting trouble, he could be expelled.
One possible reason could be that he's wrongly accused of a serious crime, like using dark magic. In the wizarding world, such accusations can lead to expulsion. Another reason might be that he's framed by a powerful enemy who wants to get him out of Hogwarts. For example, a Death Eater could plant false evidence against him.
In some fanfictions, Harry might be expelled for being wrongly accused of using dark magic. Maybe someone framed him by planting dark magic items in his dorm. Another reason could be that he continuously breaks school rules in a way that the school can't tolerate, like sneaking into the Forbidden Forest too many times without permission.
A dark wizard or witch from outside Hogwarts could be the main antagonist. They might target Harry specifically because of his reputation as the 'Chosen One' and use their influence to get him expelled from Hogwarts so that he is more vulnerable and easier to attack.
One reason could be jealousy. Harry is famous in the wizarding world, and some students might be envious of that. So they bully him to make themselves feel better.
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.
Well, it could also be that Bellatrix is simply bored with the reality of her world in the Death Eater realm. Fanfiction provides an escape into a different world where she can interact with Harry in ways that she may not be able to in the official story. It gives her a chance to be part of new and exciting (to her) adventures that revolve around Harry, even if they are just fictional interpretations created by fans.
One reason could be that she has seen his courage and selflessness. Harry is known for his heroic deeds, and Daphne might admire these qualities and thus want to protect him. Just like how people often feel the need to protect those they look up to.
One possible reason could be Lockhart's over - the - top self - promotion. In the original story, Lockhart is constantly boasting about his achievements which are actually false. In fanfiction, this could be exaggerated, making Harry see him as an untrustworthy and annoying figure, thus causing fear. Another reason might be that Lockhart could be portrayed as having some hidden and sinister motives in fanfiction, which Harry senses and is afraid of.
In the fanfic, Harry might be under a lot of pressure from the wizarding community. Everyone expects so much from him and he might feel suffocated. He could think that leaving Hogwarts and going into hiding or finding his own way to fight against evil without the constraints of school would be a better option. He wants to break free from the constant scrutiny and the pre - defined path that Hogwarts seems to offer him.
Perhaps Harry accidentally unleashes a powerful and uncontrollable magic spell within the school grounds that causes a great deal of damage. Despite it being an accident, the Hogwarts administration, fearing further chaos, decides to expel him. Harry would then have to go on a journey to learn more about this magic and how to control it, all while trying to prove to Hogwarts that he is worthy of being readmitted.