Perhaps there is a misunderstanding. In the fanfiction, other characters might have misinterpreted Peter's actions or words, and this has led to an uncomfortable situation for him. As a result, he chooses to distance himself to avoid further conflict.
One possible reason could be extreme stress. Peter Parker has a lot on his plate, being Spider - Man and having a normal life. If in the fanfiction he faces a series of really tough situations like failing to save someone important or being hunted by a very powerful enemy, the stress might get to him and lead to self - harm as a way of coping. Another reason could be feelings of isolation. Even though he has friends, he might feel like no one truly understands the dual life he leads, so in the fanfiction this could drive him to such a desperate act.
He could start by reducing his communication. For example, not answering calls or texts from other characters as often.
Some writers might do it for shock value. They want to create a very different and extreme take on the character to get a strong reaction from readers.
One reason could be extreme guilt. Maybe he failed to save someone important and can't bear the burden of that failure. In some fanfictions, if he accidentally caused harm to his loved ones, like Aunt May getting hurt because of his superhero activities, the guilt might be overwhelming.
Maybe he's been through some tough experiences like losing a friend or facing a great failure, so he needs time alone to heal. It could also be that he's discovered some dark secret about himself or his world and is trying to come to terms with it in solitude.
One possible reason could be the burden of his past. Naruto has faced a lot of hardships and the memories might be overwhelming him, making him want to be alone. For example, the loss of his master Jiraiya might have left a deep scar, and he might feel that isolating himself is the only way to deal with that pain.
Maybe he feels a sense of guilt. For example, if something bad happened in the village that he blames himself for, even if it wasn't really his fault. He could exile himself as a form of self - punishment. He has always been very hard on himself when it comes to the well - being of the village and his friends.
Perhaps he's dealing with some sort of trauma. For example, after the many battles he's been through, like the fight against Voldemort, he may be suffering from post - traumatic stress disorder. To cope with this, he isolates himself from others as he doesn't want to burden them or he's just too caught up in his own dark thoughts.
He could be exploring an old, abandoned building and fall through a rotten floorboard.
It could also be due to a sense of guilt. If something bad happened that he blames himself for, like someone getting hurt because of him, he might exile himself as a form of self - punishment. He'd rather be alone and deal with his own pain than face those he feels he's let down.