Green Goblin is also a possibility. He's always been a thorn in Spider - Man's side. He might have set up a situation where it looks like Spider - Man is the bad guy. The Avengers might be misled and Spider - Man has to hide until he can prove his innocence and stop Green Goblin's evil plan.
It could be Mysterio. He's really good at creating illusions and making Spider - Man look bad. In this case, he might be tricking the Avengers into thinking Spider - Man has done something wrong, which forces Spider - Man to hide from them.
Well, maybe he's got some secret mission that he doesn't want the Avengers to interfere with. You know, like protecting a particular person or some crucial information that he thinks the Avengers might mess up if they get involved.
It could be Doctor Octopus. He's always been a formidable foe for Spider - Man. In this fanfiction, he might have a plan that involves not just Spider - Man but also threatens the Avengers in some way, so they have to fight him to protect Spider - Man.
It could be the Green Goblin again, but this time with some new and more dangerous abilities.
The Vulture would be a great choice. His flight abilities and scavenger - like nature could pose a unique threat to the Avengers. Spider - Man already has a history with him, and it would be interesting to see how the Avengers deal with a villain who is more used to operating on a smaller, street - level scale like the Vulture.
It could be Loki. He's always causing trouble for the Avengers. He might see kidnapping a fan as a way to mess with Spider - Man and the Avengers, since he enjoys chaos and manipulation.
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.
How about a new villain created specifically for the fanfiction? A being made up of the combined negative energy from all the spider - verses. This entity could be called the 'Void - Spider' and it feeds on the chaos and destruction that often follows Spider - Man in his battles. It would be a very powerful and unique threat that the Spider - Men from different universes would have to face together.
Venom is also a strong candidate. In this fanfiction, he could be more powerful than ever. He might be infected with some sort of alien symbiote that gives him enhanced abilities. Venom could target Spider - Man because he wants to prove that he is the stronger one. And by attacking Spider - Man, he also draws the attention of the Avengers, which he sees as a challenge. He could start by attacking the city and luring Spider - Man and the Avengers into a trap.
The Green Goblin is one of the main villains. He has his own set of powers and is always causing chaos in Spider Man's city.
The Green Goblin could be a great main villain in a crossover. Imagine if he teams up with Doctor Doom from the Fantastic Four universe. Their combined evil intelligence and power would be a huge threat to Spider - Man and whoever he teams up with in the crossover.