Mysterio could be a very interesting main antagonist in a dark fanfiction. He could use his illusions to make Spider - Man question his own sanity and reality, leading him down a very dark path as he tries to figure out what's real and what's not.
Venom could also take on the role of the main antagonist in a really dark story. He could form an alliance with other villains and try to completely take over the city, with Spider - Man being the only one standing in their way.
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.
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.
Perhaps a group of dark side cultists could be the main antagonists. They idolize the power of the dark side and see Ahsoka as a prime candidate to join their ranks. When she refuses at first, they start to hunt her down, but in the process, they unknowingly push her closer to the dark side, creating a complex dynamic where they are both the pursuers and the inadvertent cause of her fall to the dark side.
A new supervillain could emerge. Maybe a scientist who got access to some of the leftover technology from the Civil War battles and uses it to create a powerful weapon. He then targets Spiderman because he represents the superhero community.
Perhaps Doctor Octopus. He might be working on a new experiment that requires a certain type of spider - DNA which Spiderman and Spider Woman possess. So he sets out to capture them, using his mechanical arms to fight them. He could be more powerful than ever, having upgraded his arms with new technology, making him a formidable foe for the two heroes.
It could be a new villain who manages to make Peter question his role as Spiderman. This villain might use mind - games or expose Peter's identity in a way that makes him want to give it all up.
The Green Goblin could be a great main antagonist. He could be causing chaos in both Spiderman and Miles Morales' neighborhoods, and they have to put aside any differences to stop him. His maniacal nature and powerful weapons would pose a great threat to both heroes.
It could be Doctor Octopus. Imagine he somehow gets his hands on some Sky High technology that enhances his mechanical arms and gives him new powers. He then decides to take on both Spider - Man and the Sky High students because he sees them as threats to his new - found power and his plans for world domination.
It could be an unknown ninja who has been secretly studying dark energon for years. He wants to use it to take over the ninja world, believing that the power of dark energon will make him invincible.
Well, obviously Dark Gaia itself could be the main antagonist. It has the power to cause chaos and destruction, and Sonic would have to stop it from wreaking havoc on the world.
It could be a powerful sorcerer. In the Dark Skies world, a sorcerer with dark magic could oppose Jesse. This sorcerer might be after the same magical artifacts as Jesse or simply wants to rule the Dark Skies with an iron fist.