A new character could be created specifically for this fanfic. A mad scientist who is obsessed with cross - species experiments. He sees Rachnera as a perfect specimen and wants to use her to create an army of hybrid creatures. He would target both Rachnera and Spiderman as they try to stop his evil plans.
The Green Goblin could be a great antagonist. His chaotic nature and advanced weaponry would pose a serious threat to both Spider - Man and She - Venom. He could be after a new power source related to the symbiote, which would bring him into conflict with our heroes.
In a 'Spiderman into the Spider - Verse fanfic', the main antagonist might be a symbiote - like creature that has the ability to infect the Spider - People across the multiverse. It spreads by attaching itself to the Spider - Sense of its victims and slowly takes over their minds. This would be a really tough enemy as it can move between universes easily. Also, it could be an ancient entity that was sealed away long ago but has now been released and blames the Spider - People for its imprisonment. It has the power to manipulate the fabric of the multiverse itself, creating all kinds of chaos. And yet another antagonist could be a rogue Spider - Woman who believes that the only way to protect her universe is to destroy all the other Spider - People, thinking they will eventually bring doom to all of them.
It could be Mysterio. He's known for his illusions and deception. In the context of a civil war, he could use his powers to create false scenarios that make the heroes fight each other even more. He might pretend to be a hero on one side, but secretly be working to make the conflict worse for his own gain.
One idea could be that Spiderman discovers Rachnera in a part of the city that's been affected by some strange scientific experiment gone wrong. He initially mistakes her for a villain but soon realizes she's just trying to find her way in this new world. They could team up to fight against the real bad guys who are behind the experiment.
Green Goblin could also work well. He could be jealous of all the attention Spiderman is getting at the homecoming and decides to crash the party. His maniacal nature would contrast well with Deadpool's zany humor and Spiderman's more responsible heroism.
A combination of Green Goblin and a chaos - causing creature from Equestria. The Green Goblin could team up with this creature and use his glider and bombs along with the creature's ability to spread chaos. They would target both Spider - Man's city and Twilight Sparkle's home, causing destruction and trying to assert their control.
It could be Doctor Octopus. He might team up with some evil spy organization. His mechanical arms and scientific knowledge combined with the sneaky tactics of the spies would make for a formidable foe for Spiderman and the Totally Spies.
It could be Doctor Octopus. He might have some new, more dangerous tentacle - like devices. He decides to target both Spiderman and female Spiderman because he views them as obstacles to his scientific experiments and his desire for power. He kidnaps some innocent people to lure them into his traps and tries to defeat them in a fight.
It could be Orochimaru. He's always been interested in unique powers and abilities. The idea of X - 23's mutant abilities and Naruto's jinchuriki powers would be very appealing to him. He might try to capture them both to use in his experiments to gain ultimate power.
The Green Goblin could be a great main antagonist in a dark fanfiction. He could be even more deranged and have a more elaborate plan to destroy Spider - Man, not just physically but also mentally by targeting his relationships.