Another reason could be related to a new prophecy. Suppose a new prophecy emerged that said Harry Potter's presence in Gryffindor would bring great danger to the house. The Gryffindor students and faculty, believing in the importance of protecting the whole house, might have decided to banish him. But of course, this would be a very difficult decision as Harry has been an important part of Gryffindor before. And in the end, the prophecy might turn out to be misinterpreted.
In some fanfictions, it could be a political move within Hogwarts. There might be a group that wants to undermine Dumbledore's influence, and since Harry is so closely associated with him, they target Harry by getting him banished from Gryffindor. This could also be related to the discovery of some long - hidden secret about Harry's family that makes the Gryffindors view him differently.
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.
In some fanfictions, it could be due to a misunderstanding. Maybe someone framed Harry for a serious rule violation that Gryffindor's house values highly, like cheating in an important magical exam. And the evidence against him seems so strong that the Gryffindor house decides to banish him.
One reason could be a personal betrayal. Maybe a close friend from Gryffindor betrays Harry, and this makes him start to dislike the whole house. It's like when one bad apple spoils the bunch in his eyes.
One reason could be a falling - out with his friends in Gryffindor. Maybe there was a misunderstanding that grew so large that he felt he couldn't stay. Another possibility is that he might be lured away by some mysterious force or character who convinces him that Gryffindor is no longer the right place for him. For example, if a new group claims to have a better way to fight Voldemort and they are from a different 'house' in this fanfiction concept.
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.
One possible reason could be a major disagreement with the Gryffindor house leadership or some of the students. Maybe he feels that they are not living up to the values he thought they held. Another reason might be that he discovers some dark secret within Gryffindor that makes him uncomfortable and he decides to leave.
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.
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.
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.