One possible reason could be a misunderstanding with his friends in Gryffindor. Maybe there was a big argument over something like a Quidditch match strategy that made him feel alienated.
It could also be due to external influence. A powerful dark wizard might be threatening him to leave Gryffindor or else harm his friends. To protect them, Harry might choose to distance himself from the house.
Perhaps he leaves Gryffindor in fanfiction because he is influenced by a new mentor or friend who is from a different house or group. This person might convince him that he can achieve more or be more true to himself outside of Gryffindor. Also, it could be due to a prophecy or a special mission that requires him to distance himself from Gryffindor for a while to protect the house or the entire Hogwarts from a certain threat.
It might be due to a self - sacrificing decision on Harry's part. He could believe that by leaving, he would protect the Weasleys from the dark forces that are constantly after him. Since he has so many enemies, he might think that as long as he is around the Weasleys, they are in danger.
One possible reason could be a difference in ideology. Maybe Peter Parker feels that Stark's methods are too extreme or not in line with his own moral compass. For example, Stark might be involved in some projects that Peter doesn't agree with, such as using certain unethical technologies in the pursuit of justice.
One reason could be that he feels ostracized. Despite his efforts to protect Konoha, some villagers still look at him with suspicion because of the Nine - Tails inside him. He might just get tired of constantly having to prove himself and decide to leave in search of a place where he can be accepted for who he is.
One reason could be that he doesn't like the spotlight that comes with being a Gryffindor. In the original story, Gryffindors are often in the limelight, and in fanfiction, he might be tired of all the attention.
One possible reason could be to escape the danger in England. Given the dark forces that were at play, especially Voldemort's rise, they might have felt it was safer to leave. Another reason could be for a fresh start. Maybe they wanted to explore new magical cultures and communities in other parts of the world.
One possible reason could be a difference in ideology. Maybe Spider - Man has a more local - friendly approach to crime - fighting while the Avengers are often involved in large - scale, global threats. He might feel that his skills are better utilized in his own neighborhood, like Queens, rather than in the grand, often cosmos - level battles of the Avengers.
One reason could be that the official Harry Potter canon is so extensive and detailed that it overshadows fanfiction. The original story has such a rich world, characters, and plotlines that it becomes the main focus for many fans, leaving less room for fan - created stories.
One possible reason could be a fallout with his friends in Gryffindor. Maybe he feels betrayed by them in some way in the fanfiction world. For example, if they wrongly suspect him of something.
Maybe he's falsely accused of stealing important Gryffindor artifacts. For instance, if the Sword of Gryffindor goes missing and Harry is wrongly blamed, the house might decide to kick him out. It could be part of a plot by a jealous student or an outside force trying to disrupt Hogwarts.