Spider - Man could lose his reputation. If the public sees the Avengers attacking him, they might assume he's done something wrong and turn against him. This could isolate him from the people he's trying to protect.
He could be seriously injured. The Avengers are a powerful group, and their combined attack would be hard for Spider - Man to withstand. He might end up with broken bones or other serious physical injuries.
There could be a storyline where Spider - Man uses his scientific knowledge to upgrade the Avengers' technology. Or perhaps a story where he has to choose between his loyalty to the Avengers and protecting his own neighborhood. This internal conflict could add depth to the fanfiction. Also, he might team up with Black Widow for a stealth mission where his agility and her skills combine for a successful operation.
One possible reason could be a misunderstanding. Maybe some villains have framed Spider - Man in a way that makes the Avengers believe he's a threat. For example, Mysterio could have created false evidence to make it seem like Spider - Man is involved in some evil plot against the world.
On the positive side, Spider - Man would have access to a whole new level of technology and training. He could learn from the likes of Captain America and Thor. However, he might also face some internal conflict within the team. The Avengers have different personalities and ideologies, and he might struggle to fit in at first. For example, he's used to being a solo hero in his neighborhood, and now he has to work with a large group of powerful individuals.
Mysterio could be the villain. He's all about creating false realities. He could be tricking the Avengers into believing Spider - Man has gone rogue. Maybe he projects false images of Spider - Man attacking the city or stealing important items, which makes the Avengers go after him.
One reason could be a misunderstanding. Maybe some events were misinterpreted, and the Avengers thought Spider - Man was involved in something bad. For example, if there were some crimes that seemed to have Spider - Man's fingerprints all over them, but in reality, he was being framed.
Some Avengers might be protective. For instance, Captain America could immediately start giving Peter advice on how to better handle his dual identity and keep himself safe. He might offer training sessions to help Peter improve his skills as Spider - Man.
The experiment could also make him an outcast. If the changes are too extreme, his friends and the public might be afraid of him. He would have to deal with the loneliness and the struggle to prove that he is still the same Spider Man at heart, just with some new abilities or features.
Perhaps there's a new law or regulation in the superhero world that Spider - Man has broken, unknowingly. The Avengers, being the enforcers of sorts, attack him. Like, there's a rule about using certain powers in public and Spider - Man accidentally did it while saving people. The Avengers misinterpret his actions as blatant disregard for the law.
There could be a redemption arc in the fanfiction. Spider - Man might work hard to prove himself and clear his name. He could start by taking on smaller threats and gradually build his reputation back up. This might involve him saving the day in a very public way, which catches the attention of the Avengers again. Eventually, he could be reinstated into the team, but with a new - found respect for the importance of trust and loyalty within the group.
Some Avengers might be surprised. Tony Stark, for instance, might be like 'Kid, you're younger than I thought!' and then start to adjust how he mentors Spider - Man. He could become more cautious about the risks he lets Spider - Man take.