It could be that his friends are going through their own personal issues. They might be so preoccupied with their own problems, like family troubles or difficulties in their studies of magic, that they unconsciously start to ignore Harry. Also, there could be a new character in the fanfiction who is influencing his friends to distance themselves from Harry, perhaps by spreading lies or by being overly charming and manipulative.
One reason could be jealousy. Maybe Harry has achieved something great like getting a special magical power or a high honor in their magical world, and his friends feel envious. Another reason might be a misunderstanding. For example, Harry could have been wrongly accused of something, and his friends believe the false rumors without giving him a chance to explain.
Perhaps the fanfiction is following a specific plot arc that doesn't naturally involve Stiles. Like if it's a story about a new villain in town and the existing characters are dealing with it in a way that doesn't require Stiles' skills or presence. Also, some writers might be influenced by popular trends in the fandom that don't feature Stiles, and they go along with that to attract more readers.
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 possible reason could be jealousy. Maybe Naruto has been getting more attention from the village elders or teachers because of his potential. His friends, feeling left out or overshadowed, might start to ignore him out of envy.
One possible reason could be jealousy. Maybe his friends become envious of Harry's growing powers or popularity. For example, if Harry is suddenly getting all the attention in their magical community, his friends might feel left out and start to resent him, leading to betrayal.
If his friends continue to ignore him, Harry could become sad and withdrawn himself. He might start to isolate more, spending time alone in places like the Forbidden Forest or an empty classroom. He might also lose his confidence in himself, thinking that he is not worthy of their friendship. In his loneliness, he could focus more on his studies or some solitary magical pursuits, trying to distract himself from the pain of being ignored.
One possible reason could be that he is wrongly accused of using dark magic. In some fanfictions, the Ministry of Magic might be more corrupt or easily influenced, and they could frame Harry for something he didn't do, leading to his expulsion.
Well, in some fanfictions, it could be because of a curse or a jinx that was unknowingly placed on him before he arrived at the Burrow. The Burrow is not always a completely safe place, and with all the comings and goings of wizards and witches, someone with ill intentions could have targeted Harry. Also, he might have eaten something that didn't agree with him. The Weasley family's cooking, while delicious most of the time, could have used some ingredients that Harry's body wasn't used to.
One common reason is his determination. Harry has always been a fighter, and in fanfiction, he could transfer that tenacity to his studies. He simply refuses to be bad at academics and works hard to prove himself.
One reason could be that he has a change in motivation. Maybe he realizes that good grades can help him achieve his long - term goals, like becoming an Auror. So he starts to put in more effort into his studies.
Naruto might initially feel sad and confused. He could try to prove himself to his friends by working hard on his ninja skills. For example, he might train extra hours to show his friends that he is worthy of their attention.