There's a possibility that a new villain emerges from the power dynamics created by the One Above All's presence. This villain might be a twisted version of Spider Man himself, created by some sort of dark magic or science gone wrong during the encounter. The main villain could also be an ancient force that has been locked away for eons and is released because of the commotion caused by Spider Man and the One Above All meeting. It could be a force that wants to destroy the balance that the One Above All has maintained.
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.
In this fanfiction, Spider Man might gain some ultimate knowledge or power from the One Above All. Maybe he'll be faced with a huge cosmic threat that only with the One Above All's help can he overcome.
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.
The Vulture could also be a major antagonist. His ability to fly and his sharp talons pose a great threat. Maybe he teams up with some other villains in the fanfiction to take on the two spiders at once. He could be stealing valuable items from around the city and Spider - Man and Spider - Gwen have to stop him.
It could be Voldemort still. He would be really interested in Mega Man's technology and try to use it for his own evil purposes. Maybe he wants to combine magic and technology to create an unstoppable force.
Maybe the Vulture. He's always on the lookout for new tech to sell on the black market. When he hears about Ant Man's unique shrinking abilities, he decides to capture Ant Man and force him to reveal his secrets. Spider Man steps in to protect Ant Man, and they have to fight the Vulture together.
In fanfiction, their powers could interact in a way that defies the normal rules of the Marvel universe. Maybe Spider - Man's power to stick to surfaces could be transferred to Female One - Above - All in a way that gives her an advantage in a particular battle. Or perhaps she could use her power to manipulate reality to give Spider - Man a new form of his powers, like the ability to fly temporarily. Their combined powers could also lead to the creation of new, unique abilities that are a blend of their individual powers, such as a web - like energy projection that can hold even the most powerful enemies at bay.
Perhaps there's a fanfiction where Spider - Man discovers a connection between his powers and the origin of Female One - Above - All. This could involve some sort of ancient prophecy or hidden knowledge. As they explore this connection, they find that they are part of a bigger plan. Along the way, they encounter other characters from the Marvel universe who either help or hinder their journey to uncover the truth.
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.
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.