Maybe a biologist gone bad. He has been studying the worm and discovers that its cells can be used to create a powerful mutagen that can turn ordinary people into super - strong minions. He plans to create an army and take over the city. Spiderman has to stop him from using the worm in this way. And the worm, being an innocent creature, becomes a key piece in this battle between good and evil.
The Green Goblin could be a great main villain. He could be working on a plan that not only threatens Spider - Man's world but also the areas the Defenders protect. His maniacal nature and flying abilities would pose a great challenge to both Spider - Man's acrobatics and the Defenders' combat skills.
A possible plot could involve a mad scientist who combines the DNA of a worm with some sort of mutagen that gives it super - human like intelligence and abilities. This new 'worm - creature' starts causing chaos in the city. Spiderman, being the friendly neighborhood hero, investigates. He discovers that the worm - creature is not entirely evil but just confused. So, he tries to help it while also protecting the city from its accidental destruction.
The Green Goblin could be a great main villain. He has a long - standing feud with Spiderman, and when the Avengers get involved, it could make the situation even more complex. His flying glider and pumpkin bombs would pose a serious threat to both Spiderman and the Avengers.
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.
Doctor Octopus would also work well. He could use his mechanical arms to manipulate the game environment and create deadly traps for Spiderman, all while trying to steal some valuable in - game technology.
Kingpin would be a very suitable main villain. He has his criminal empire in Hell's Kitchen already, and if he decides to make a move on Gotham, it would bring him into conflict with Batman. His power, wealth, and ruthlessness would make him a formidable foe for the two heroes to face together.
The Joker would be really interesting. Imagine him getting his hands on some of Oscorp's dangerous technology. He could use it to create chaos in both Gotham and New York in ways that neither Batman nor Spiderman have seen before. His unpredictable nature would make it hard for the two heroes to anticipate his moves.
Madara Uchiha could be a great main villain in such a crossover. His already powerful ninja abilities combined with the potential of getting a Geass power would make him extremely dangerous. He could use Geass to control other ninjas and make them fight for his cause, like creating an army of mind - controlled shinobi to take over the world.
A powerful dementor - like being that has been corrupted by Asgardian dark magic. This entity could be draining the life force of both wizards and Asgardians. It would be up to Thor and Harry Potter to find a way to stop it, as it poses a threat to both of their worlds.
A young and curious Pokemon trainer would be a great main character. This trainer could be someone who is always on the lookout for rare and unique Pokemon. When they encounter the worm - like Pokemon, they are immediately intrigued and decide to make it a part of their team.