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 possible plot could be that Harry is framed for something he didn't do. Maybe a powerful dark object is found in his dorm, and the Gryffindor house, fearing for their reputation and safety, decides to exile him. Harry then has to prove his innocence while also dealing with the isolation and new challenges outside of his familiar house.
A dark force that has the ability to influence the minds of Gryffindor members. This could be a powerful and ancient magic or a new form of dark magic. It turns the house against Harry without them fully realizing it, making the collective Gryffindor house, under this influence, seem like the antagonist.
He would probably be extremely hurt. Gryffindor was like his family at Hogwarts, so being exiled would be a huge blow. He might initially feel angry and betrayed.
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.
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.
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 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.
Maybe he was too busy dealing with the real threats in his life, like Voldemort and his Death Eaters. Fanfiction might seem unimportant compared to the real battles he had to face.
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.