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.
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.
In this fanfiction, it might be that Peter has been framed for a crime he didn't commit. The Avengers, who are duty - bound to uphold justice, are misled by false evidence. They attack Peter, but as the story progresses, Peter tries to prove his innocence. He might find some allies within the superhero community who believe in him and help him face the Avengers and clear his name.
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.
It could be Mysterio. He's a master of illusions. He might trick the Avengers into believing that Spiderman is a danger, using his illusions to make it seem like Spiderman is doing bad things. So the Avengers, thinking they're doing the right thing, kidnap Spiderman.
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.
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.
Loki could be a likely villain. He has a history of mind - controlling people and causing chaos within the Avengers. He might see Hawkeye as a useful tool to disrupt the team again. His mischievous nature and magic powers would make it easy for him to brainwash Hawkeye without being detected at first.
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.
Maybe the Vulture could make a comeback. In this fanfiction, he might be out of prison and looking for revenge on Peter. Or it could be a new villain that has heard about the young Spider - Man patrolling alone and sees it as an opportunity to take him down. And of course, there's always the possibility of Aunt May finding out more about his solo patrols and getting worried.