It could also be due to some sort of potion he accidentally consumed. In the wizarding world, there are all kinds of potions. He might have mistaken a dangerous potion for something else. For example, if he drank a sleeping draught that was too strong or had been tampered with. There could also be a plot where someone wants to stop him from reaching Hogwarts, so they slip him this potion.
Perhaps he was having a vision related to his connection with Voldemort. In the original series, Harry had such connections. In fanfiction, this could be expanded. The vision could be so intense and disturbing that it causes him to pass out. It might be a new kind of vision that he hasn't experienced before, related to a hidden threat to Hogwarts or his friends.
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.
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.
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.
In some fanfictions, there could be a change in the Hogwarts admission policy. Maybe they found some supposed flaw in Harry's magical abilities or his background that led to his admission being revoked at the last minute, so he didn't arrive at Hogwarts. Also, it's possible that some other powerful magic was at work. A powerful wizard or witch could have cast a spell on Harry that made him forget about Hogwarts or made it so that he couldn't physically reach the school.
One reason could be that he doesn't like others taking creative liberties with his story. He might feel that it's his story and only the original version should be the 'true' one.
One possible reason is that she might be anemic. Lack of enough iron in the body can lead to anemia which may result in fainting spells. Standing up too quickly can also cause a drop in blood pressure and make her pass out, this is called orthostatic hypotension. Additionally, certain medications she might be taking could have side effects that lead to fainting.
One reason could be that he's being hidden by some powerful magic from a group that wants to use him for dark purposes. Maybe there are dark wizards who know of his future importance and want to either kill or control him, so a good wizard has made him disappear.
One reason could be to search for a powerful magical artifact outside of Hogwarts that they believe is crucial for defeating a new dark threat. In fanfiction, they might feel that Hogwarts has become too dangerous or restricted in terms of resources for their mission.
Maybe he leaves because of a conflict with the Hogwarts staff. If the new headmaster or some teachers start implementing rules that Harry believes are wrong or unfair, like restrictions on defensive magic classes, he might decide to leave in protest.
One reason could be that he has fallen in love with someone outside of Hogwarts and wants to stay with that person instead. He may feel that Hogwarts will keep him away from his beloved.
In fanfiction, the author might want to explore a different side of Harry. He could be berating Hogwarts education because he realizes that some students were left behind. There were students like Neville who didn't really shine until later, and Harry might think that the school system should have been more inclusive and better at nurturing all types of magic abilities from the start.