Perhaps there's a new character in the fanfic who has a vendetta against Harry and manages to manipulate the situation in such a way that Harry gets framed for something serious. This new character could be from another house or have some sort of hidden agenda. They might spread rumors or create situations where it looks like Harry is endangering the other students in Gryffindor, causing the house to expel him.
It could be due to a series of bad decisions that made him seem like a bad influence in Gryffindor. For example, if he constantly got into fights with other Gryffindors and disrupted the harmony of the house, they might kick him out. Also, if he was caught breaking too many school rules in a way that reflected poorly on Gryffindor as a whole, like sneaking out at night to go to the Forbidden Forest too often without a good reason, that could lead to his expulsion.
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 reason could be that he breaks a major school rule. For example, if he uses dark magic without proper authorization, the Gryffindor house might decide to expel him. Gryffindor values courage, but there are limits, and using dark magic goes against the values of the school as a whole.
One possible reason could be a serious rule violation. For example, if Harry was wrongly accused of using dark magic within the Gryffindor common room. Another reason might be that he was framed for stealing the Gryffindor sword. It could also be due to a conflict with other Gryffindor students that got out of hand and the house decided they couldn't keep him anymore.
Ginny could first be in shock. But then, she would start thinking of ways to help Harry. She could offer him emotional support, like being there for him when he is feeling down about being expelled. She may also try to rally their mutual friends to support Harry, whether it's by protesting the decision or by helping him find a new place to belong in the school.
In some fanfictions, if Harry is kicked out of Gryffindor, he might end up joining another house like Hufflepuff. The Hufflepuffs are known for their acceptance and might welcome Harry with open arms. This could lead to a whole new set of adventures for Harry, as he would have to adjust to the different values and culture of Hufflepuff house.
If Harry was kicked out of Gryffindor in Ginny - related fanfiction, Ginny would likely be one of the first to oppose the decision. She might secretly help Harry by providing him with a place to stay in Gryffindor's common room undetected. And she could start her own investigation into what really happened, suspecting foul play. After all, Harry has been a hero in Gryffindor and Ginny wouldn't let him be cast out so easily.
Hermione would probably be outraged. She would immediately start investigating the situation to find out the truth. She'd be convinced that there has been some sort of mistake or foul play. She might even go as far as to confront the teachers or the Gryffindor house leaders about it.
Maybe he was blamed for some trouble he didn't actually cause. For example, if something went missing in the orphanage and the caretakers wrongly thought Naruto took it.
One reason could be causing disruption. If the 'crusade' involved making a lot of noise, blocking hallways, or disturbing classes, the school would likely take action.
One reason could be that the fanfic distorts the characters he knows well from Gryffindor. For instance, if it changes the personalities of his friends in Gryffindor in a way that doesn't seem right to him.