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.
It could be that the writer has a personal preference for other characters. If they are more drawn to the personalities or storylines of characters other than Stiles, they may unconsciously or deliberately ignore him. Additionally, in some cases, if the fanfiction is a crossover and the new elements from the other universe don't mesh well with Stiles' character, he might get left out.
One possible reason could be a power struggle. Gerard might see Stiles as a threat to his own authority or plans within the story's context.
Well, in a lot of these fanfictions, Stiles can get beat up due to his own recklessness. He might be so determined to solve a mystery or help his friends that he doesn't think about the consequences and ends up in a dangerous situation where he is outnumbered and beaten up. Also, there could be miscommunication. Maybe someone thinks he has done something wrong when he actually hasn't, and they take matters into their own hands and beat him up.
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.
Some writers might be exploring dark themes for the sake of drama. They think it can create intense emotions and complex character arcs.
One reason could be that he's tired of always being in the background. In the pack, others with more obvious powers might overshadow him. So he decides he's done and wants to find a place where he can shine on his own.
One possible reason could be that Peter has a certain allure of mystery. Stiles is a curious character, and Peter's complex past and often ambiguous motives might draw Stiles in. Peter also has a more unorthodox way of dealing with things, which could seem exciting compared to Scott's more straightforward approach.
One possible reason could be jealousy. Maybe some members of Team 7 are jealous of Naruto's natural talent that he doesn't even realize he has. Another reason might be a misunderstanding. Naruto is often brash and loud, and his teammates could misinterpret this as him being over - confident or show - offish, when in reality he's just trying to prove himself. Also, there could be a pre - existing bias. If some members of Team 7 come from more 'privileged' ninja families, they might look down on Naruto who was an outcast in the village for a long time.
Perhaps Stiles is killed as a sacrifice in a dark ritual. His death could be part of a much larger conspiracy. His friends might start seeing strange visions of him after his death, which they initially think are just their minds playing tricks on them, but later realize are actually Stiles trying to communicate from the afterlife to help them stop the forces behind his death.
One possible reason could be to protect his friends. Maybe he discovers a new threat that is specifically targeting him, and he decides to leave Beacon Hills to draw the danger away from those he loves. For example, in some fanfictions, a powerful and vengeful supernatural being might be after Stiles, and he believes that by leaving, he can keep his friends safe.
One possible reason could be that he feels he's a liability to the pack. Maybe he doesn't have the same supernatural abilities as the others and fears he'll hold them back during dangerous situations.