The Green Goblin could be the villain. He could have developed a new type of pumpkin bomb that explodes with a force that seriously injures Spider Man. This would be in line with their long - standing rivalry in the Spider - Man universe.
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.
Perhaps a new character, like a genetically - engineered super - soldier gone wrong. This villain could have super strength and agility similar to Spider - Man, but with a more aggressive and unpredictable nature. He might see Spider - Man as a rival and be determined to prove that he is the superior one in the city.
One interesting villain Spider - Man fanfiction could be where the Green Goblin actually teams up with Spider - Man to take on a greater threat from another dimension. It flips the typical dynamic on its head.
Perhaps Sabretooth could be the villain. He might be targeting Wolverine specifically, but his actions in a big city draw Spider - Man's attention. Sabretooth's savage nature and powerful claws would pose a great threat. Spider - Man and Wolverine would have to work together to defeat him, with Wolverine having the personal vendetta and Spider - Man the sense of justice for the city.
Mysterio could also be a villain in this scenario. He could use his illusions to make the people of New York lose hope. Since Spider - Man has the Blue Lantern powers of hope, Mysterio would see him as a threat. He could create elaborate illusions that make it seem like the Blue Lanterns are a force of evil, causing chaos and making Spider - Man's job of spreading hope and protecting the city much more difficult.
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.
Well, in the Spider - Man universe, one common factor could be personal tragedy. Maybe the person lost someone dear due to Spider - Man's actions, whether intentional or not. For example, if a bystander was accidentally hurt during one of Spider - Man's battles and that person was a loved one of the future villain, it could fuel their hatred and desire for revenge. Another aspect could be envy. Spider - Man has all these amazing powers and is adored by the public. Someone who feels overshadowed and unappreciated in comparison might turn to villainy just to prove themselves and get the attention they think they deserve.