There are several villains that could be behind it. Kraven the Hunter might be a likely choice as he's always after the most challenging prey, and Peter would be a great target for him. Another could be Doctor Doom if he decided to make a move against the Avengers. He could use pushing Peter off the roof as a way to test the Avengers' defenses. And then there's the Vulture. Even though he had his own story, he could return and, out of jealousy or revenge, push Peter off the roof, especially if he thought Peter was getting too much attention from the Avengers.
One possible villain could be Loki. He's always up to his mischievous ways and might see pushing Peter off the roof as a way to disrupt the Avengers. Another option is Ultron. Even though he was defeated, his remnants could be programmed to target the youngest Avenger. And of course, there's always the Green Goblin. If he somehow made his way into the Avengers universe, he'd be a likely candidate to target Spider - Man.
One possible storyline could be that Peter survives the fall but has to deal with the psychological trauma. He might start to question his place in the Avengers and whether he's really cut out for this superhero life. Another could be that he is saved by an unexpected ally, like Doctor Strange who uses his magic to break his fall. And then there's the idea that his fall sets off a chain of events that makes the Avengers re - evaluate their security and how they protect their youngest member.
It could be Mysterio. He's known for his illusions and deception. He might create false scenarios that make the Avengers think Peter is a threat. He could manipulate the Avengers' perception of Peter's actions, like making it seem like Peter is causing destruction when he's actually trying to help.
Perhaps they call Peter in class because they've discovered some sort of conspiracy that involves the school or someone in it. Peter, being a friendly neighborhood Spider - Man, has a good sense of what's normal and what's not in his neighborhood which includes the school. They might need his help to investigate something strange going on within the school walls.
Thanos could also be a good option. Imagine Bella's planet holds one of the Infinity Stones that Thanos needs. He would stop at nothing to get it, and Bella and the Avengers would have to join forces to protect it. Thanos' brute strength and strategic mind would pose a huge challenge for them.
A powerful necromancer could be a great main villain. He tries to control the ghostly avengers for his own evil purposes, using dark magic to manipulate them.
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 a more fantastical setting, it could be a magical being who has some sort of vendetta against Peter or Michelle. Maybe they accidentally disrupted some magical ritual or offended the being in some way, and now the being wants to use their kidnapping as a form of punishment or to get something from them.
It could be about a hero - in - training who is constantly bullied because they haven't developed their quirk yet. The constant harassment makes them feel so low that they consider a swan dive off the roof as an escape from the pain.
One possible reason could be that Jiraiya was trying to test Naruto's survival skills. He might have thought that by pushing Naruto off the cliff, Naruto would be forced to use his ninja skills in a real - life - or - die situation and grow stronger as a result.
One option is Pepper Potts. She is intelligent and has a strong will. In a fanfiction, she might see the potential in Peter and they could develop a relationship. Pepper could also help Peter deal with the business side of being a superhero, like Tony Stark did, and they could fall in love over time.