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.
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.
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 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 wants more independence. In many fanfics, characters like Harry might feel restricted at home and long for the freedom to make their own choices, so that could be a reason for him to move out.
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 passing out can also be a way to introduce new plot elements. Maybe when he's unconscious, he has strange dreams or visions that point to a new mystery or threat. This can then drive the rest of the story as the characters try to understand the meaning of these visions and prevent the potential danger.
One reason could be that he was under a dark spell cast by a new enemy in the fanfiction. Maybe some dark wizard or witch sent a spell his way before he boarded the train, and it took effect during the journey.
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 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.