It could also be due to extreme exhaustion. Harry often gets involved in intense battles or has to endure long periods of stress. For example, if he's been fighting multiple foes continuously without a break, his body and magic might give out, leading to him passing out.
One possible reason could be a powerful spell backfiring on him. In fanfiction, authors often play around with magic going wrong. Another reason might be extreme emotional distress. For example, if he discovers something truly shocking about his past or his friends.
It could be due to some kind of extreme emotional shock. For example, if he discovered something really horrible or had a sudden and intense encounter with an enemy, it might have been too much for him to handle and he passed out.
Another reason might be related to a new piece of technology. For example, if there was a malfunction in some experimental Stark Industries device that emitted some sort of energy wave. Pepper, being close to it, could have been affected and passed out as a result.
One possible reason could be that he felt he had learned enough magic to face his enemies on his own. He might have thought that the traditional Hogwarts education was too slow or not relevant to his specific needs, like dealing with Voldemort. Another reason could be some sort of conflict with the Hogwarts faculty. Maybe he didn't agree with their methods or decisions and decided he was better off without their rules.
One possible reason could be that in the fanfiction, the wizarding community in England has turned against Harry due to some false accusations. Maybe a powerful dark wizard has framed him for a series of heinous crimes, and the public, being misled, forces him to leave. Another reason might be political intrigue within the Ministry of Magic. There could be a new regime that sees Harry as a threat to their power and thus kicks him out.
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 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.
Well, perhaps in the fanfiction, Harry has a vision of a different future for himself that doesn't involve traditional Hogwarts education. He might have seen a path where he can make a greater impact on the wizarding world without the constraints of school. It could also be that he's being influenced by a new character in the fanfiction, someone who convinces him that there are better ways to develop his magic and knowledge outside of Hogwarts. This new influence could be from a different magical culture or a rogue wizard with unique ideas.
His friends might be involved in some way. They could be trying to protect him but something goes wrong and Harry ends up passing out. For instance, they might be using a spell to shield him but it backfires.
One possible reason could be a misunderstanding. Maybe Percy was wrongly accused of something, like stealing an important item in the fanfiction world, and Sall, being impulsive, kicked him out without proper investigation.