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.
Loki could be a great main villain. He could trick Spider - Man into believing that Thor is a threat to Earth and set them against each other. Then, while they are fighting, Loki could carry out his real plan which might involve stealing a powerful artifact from both Asgard and Earth.
Mysterio could be an interesting main villain. He could use time travel to create elaborate illusions across different time periods. Spider - Man would have to figure out which events are real and which are Mysterio's illusions while also trying to stop him from causing chaos throughout time.
Maybe a fanfiction where all the Spider - Men and Women from different spider - verses team up to fight a common enemy that threatens all of their universes. It could be a powerful cosmic entity that is consuming the multiverse, and they have to combine their unique skills and knowledge to stop it. This would allow for a lot of cool interactions between the different characters.
The main characters include Miles Morales, who is a key figure as he discovers his powers and tries to fit into the world of Spider - Men. Peter B. Parker, an older and more jaded version of Spider - Man, is also important. Gwen Stacy, as Spider - Woman from another universe, is among the main characters too. Their interactions and different personalities drive the story forward.
Penni Parker could be a great focus. In the movie, she doesn't get as much screen time as some of the others. Fanfiction could explore her backstory more, like how she became the SP//dr in her universe and what her daily life is like when she's not in the multiverse - saving action.
Gwen Stacy is an obvious choice. In different universes, she has different relationships with Spider - Man. Another could be Mary Jane. She has always been an important part of Spider - Man's life. Black Cat might also be in the harem as she has a complex and flirtatious relationship with Spider - Man in the comics.
Maybe a villain who can transform into different animals. He could use this power to stalk Spider - Man in the city, changing forms to blend in and then attack when least expected. This would keep Spider - Man on his toes as he tries to figure out the pattern of the villain's attacks and how to counter this shape - shifting ability.
One possible fanfiction could be about Venom finding its way into the Spider - Verse. Maybe it starts when a symbiote experiment in an alternate dimension goes wrong and Venom is accidentally sent into the Spider - Verse. He could encounter different versions of Spider - Man and create chaos as he tries to find a way back to his own dimension. He might initially be seen as a threat by the Spider - People, but as the story progresses, they could realize that he's just lost and confused.
Miles Morales is one of the main characters.
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.