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.
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.
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.
In some fanfictions, the author might create a situation where Harry's actions lead to great harm to Gryffindor as a whole. For instance, if he makes a decision that causes Gryffindor to lose a significant amount of points in a crucial time, like right before a major competition. This could lead to his censure as the house would see him as a liability. Also, if he gets into a feud with important Gryffindor figures, like the prefects or the head of the house, it could result in his censure.
One possible reason could be a false accusation of using dark magic. In some fanfictions, the wizarding world can be very paranoid about dark magic, and if Harry was wrongly suspected of delving into it, Gryffindor might exile him to protect their reputation.
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In some fanfictions, Harry could become withdrawn and depressed at first. Losing his place in Gryffindor is like losing his family. But then, he might find new strength and purpose, perhaps by joining forces with some outcasts in the wizarding world and forming a new group that challenges the unjust actions of Gryffindor house.
He might feel a great sense of betrayal. Since Gryffindor was like his home in Hogwarts, being banned could make him question his identity. He could become more isolated and withdrawn at first. However, this could also lead to him finding new friends and allies from other houses or even outside of Hogwarts.
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.