It could be that an outside force is controlling Peter in some way, like a powerful villain using mind - control. Peter, realizing he's a danger to the Avengers while under this influence, decides to flee to protect them.
One possible reason could be that Peter is being framed for something. Maybe there's a misunderstanding where evidence is planted to make it seem like he's betrayed the Avengers, so he flees to clear his name.
Perhaps Peter discovers some dark secret within the Avengers that he's not supposed to know. This knowledge makes him fear for his life or the safety of others he cares about, leading him to flee. For example, if he finds out about a dangerous experiment they're conducting secretly that could harm civilians.
Well, it could be his age. Peter is relatively young compared to the other Avengers. They might assume that a young person in their highly - secure area is an intruder. Also, if he showed up at a time when they were on high alert, like after some threat or security breach, they'd be more likely to suspect him. For example, if there had been a break - in attempt recently, and then Peter just swings in out of nowhere.
One possible reason could be that they are framed for a crime they didn't commit. Maybe some powerful and malicious forces within Konoha set them up to take the blame for something big, like a failed mission that was actually sabotaged by others.
One possible reason could be overexertion. Peter Parker is often depicted as taking on a lot of responsibilities both as Spider - Man and as an Avenger. He might be pushing himself too hard in a fight or during a mission, leading to a collapse. Another reason could be some sort of external attack that affects his physical or mental state, like a new type of villain's weapon that drains his energy.
One possible reason could be a misunderstanding. Maybe Peter accidentally gets involved in something that looks bad to the Avengers, like being in the wrong place at the wrong time during a security breach. So they misjudge him and are mean as a result.
In fanfiction, Harry could flee Britain due to a sense of disillusionment with the wizarding world there. He has been through so much trauma and has seen the flaws in the system. For example, the way the Ministry handled the threat of Voldemort in the past was often inept. He might also be seeking a place where he can explore magic in a different way, free from the traditional constraints of the British wizarding community. He may want to start anew in a place where no one knows him as 'The Boy Who Lived' and can just be Harry, an ordinary wizard exploring his magical abilities.
Maybe Peter was in some kind of trouble at school and they needed to rescue him.
In some fanfictions, Peter could have a secret that he's keeping from the Avengers. When it's eventually revealed, they might feel betrayed and turn against him. It could be something related to his powers, or his past associations that the Avengers find unacceptable, thus resulting in their hatred.
One possible reason could be that Peter might feel like he's a burden to Tony. Maybe he made a big mistake and is afraid of Tony's reaction. For example, if he accidentally endangered the lives of others during a mission while under Tony's supervision.
It could be a result of a genetic mutation that is unique to the fanfiction world he is in. This mutation might be triggered by extreme stress or exposure to certain substances, causing his eyes to bleed. For example, if he has been in an area filled with some strange radioactive - like substances that affect his body in this unusual way.
One way is by getting involved in Peter's school life in a more official capacity. Maybe they could arrange for some anti - bullying seminars at the school. Natasha could also train Peter in stealth and evasion techniques so that he can avoid the bullies more easily. Thor could even offer to be Peter's bodyguard for a while, at least until the bullying situation is resolved.