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.
In such fanfiction, one interesting aspect could be how Iron Man mentors Spider - Man in the ways of being a superhero. Maybe he teaches him about advanced tech - based combat strategies that are unique to Iron Man's style.
Maybe some new villains from the multiverse. As Loki and Peter start exploring different realms together, they could encounter beings who want to use Peter's powers for their own evil plans. These villains might be powerful magic - users or creatures that are not from Earth and have different motives and abilities.
In the Naruto world, it could be Orochimaru. He might be interested in Naruto's newfound Pokémon - related powers and try to capture him to experiment on him. Orochimaru is always after power, and Naruto's unique abilities could be very appealing to him.
One possible main antagonist could be Frieza. Imagine if Frieza somehow found his way into the Naruto universe. He would be attracted to the chaos and power struggles there. Goku and Naruto would have to team up to stop him from taking over the Naruto world. Frieza's cold - blooded nature and his desire for power would put him at odds with our heroes. His powerful abilities would be a huge threat to both Naruto and Goku, especially since Naruto is still learning about the new powers Goku is teaching him.
Another possibility is that some rogue ninja who have a vendetta against Hanzo might target Naruto as a way to get back at Hanzo. They could see Naruto as Hanzo's weakness and try to harm or kidnap him, which would then lead to a series of battles and confrontations in the fanfiction.
The main antagonists could be the traditional enemies of Camelot like Morgana. She might see Merlin's act of adopting Mordred as a threat to her plans. Also, some of the knights or nobles in Camelot who are superstitious and believe Mordred is a danger just because of the prophecies could be antagonists. They might try to separate Merlin and Mordred or even harm Mordred.
Loki could be a great antagonist. He could use his own time - traveling magic to counter Iron Man's attempts at fixing the timeline. Maybe he wants to create chaos in different time periods for his own amusement or to gain power. Another could be an evil version of Iron Man from an alternate timeline, who doesn't have the same moral compass and wants to take over all timelines.
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 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.