Doctor Octopus can also be a key antagonist in these stories. His intelligence and mechanical arms make him a formidable foe. He might create situations where Spiderman is forced to make difficult choices, and if those choices go wrong, it can send Spiderman into a downward spiral of self - doubt and darker actions.
It could be a new super - villain created specifically for the fanfic. Maybe a scientist who has developed a formula that gives him the ability to manipulate energy and he wants to use it to take over the city. His powers would pose a threat to both Spider - Man and She - Hulk.
It could be Venom. Since Venom is often associated with the symbiote in the Spiderman universe, he might be trying to keep the symbiote for himself and use its power for evil. So he would be a major antagonist in the story of Spiderman trying to get the symbiote back.
Mephisto could also be an antagonist. He might be interested in Scarlet Witch's reality - warping abilities and try to corrupt her. Spider - Man would then have to try and save her from Mephisto's clutches while also dealing with the devil's minions. Mephisto could use his powers of illusion and manipulation to drive a wedge between them.
Another possible antagonist could be Doctor Octopus. His brilliant mind and powerful mechanical arms would give Iron Man and Spider - Man a tough fight. He might be after some technology that Iron Man has or be trying to prove his superiority in the scientific and criminal world, which would bring him into direct conflict with our heroes.
Maybe Mysterio. He could create illusions that make it difficult for Spiderman and Wasp to tell what's real and what's not. He might be trying to steal their powers or something related to their superhero identities. His ability to deceive would be a major obstacle for them to overcome.
One possible main antagonist could be an ancient evil that has been awakened by the discovery of the Dark Excalibur. This entity might be seeking to use Sonic as a pawn to spread chaos and destruction. For example, it could be a long - forgotten dark wizard who once forged the Excalibur for evil purposes.
The main antagonists might be a new breed of ninja created by some dark jutsu or experiment within the 'dark empire' fanfiction. These new ninjas could have powers that are a threat to Naruto and his friends, and they are bent on spreading chaos and darkness throughout the Naruto world. They might have no moral compass and be solely focused on domination.
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.
The Hidden Leaf Village elders could be antagonists. If Naruto turns dark, they might see him as a threat to their power and try to stop him. Their actions against Naruto could further fuel his descent into darkness.
Heretek Tech - Priests are antagonists too. They have deviated from the proper teachings of the Adeptus Mechanicus and are using their knowledge for heretical ends, like creating unholy machines or corrupting existing technology, which can pose a great threat to the Imperium.