Maybe it's an old enemy who has a new plan. For instance, the Green Goblin could find a way to make Peter's life so miserable as Spiderman that he just can't take it anymore. He might target Peter's friends or family in a more extreme way than before, leading Peter to believe that being Spiderman is only bringing harm.
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.
Maybe Peter gets tired of the double life. He realizes that being Spiderman has cost him too much, like his normal relationships or his own mental health. So he decides to give up the mantle.
It could be a new character introduced in the fanfiction. Maybe a powerful witch who has the ability to manipulate emotions. She targets Stiles and makes him stop caring as part of her evil plan to disrupt the balance in the town. Since Stiles is an important part of the group, his change in attitude would cause chaos.
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.
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.
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.
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.
A powerful dark wizard could be the main antagonist. This wizard has been ruling the other dimension with an iron fist and sees Peter as a threat to his power. He uses his dark magic to create all kinds of obstacles for Peter, from summoning monsters to casting spells that distort Peter's perception of reality.
A powerful and corrupt organization might be the main antagonist. They blackmail Wade into kidnapping Peter. The organization wants to study Peter or use him as a bargaining chip. Wade is caught in a difficult situation where he has to protect Peter from this organization while also dealing with the fact that he has kidnapped him.