The main antagonist could be a new character, a rogue Sky High student who has turned bad. This student has a power that allows them to manipulate minds and they team up with some of Spider - Man's classic villains like the Green Goblin. Together, they plan to create chaos in both the Sky High world and New York, forcing Spider - Man and the remaining good Sky High students to stop them.
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.
Maybe in this fanfiction, the technology or magic from Sky High somehow gets mixed up with the science in Spider - Man's world. For example, a device from Sky High that controls powers malfunctions and starts affecting Spider - Man's powers. He has to team up with some Sky High students who are good at tech - magic stuff to fix it and in the process, they have to fight off some enemies who want to use this power - mix - up for their own evil plans.
Venom could be a main antagonist in this crossover. If Venom were to find his way to Gotham, he would be a formidable foe. His strength and aggression combined with his alien symbiote abilities would make him a tough opponent. Batman would have to rely on his gadgets and strategic thinking, while Spiderman, having prior experience with Venom, would have to use his knowledge of the symbiote to try and stop it. And Venom's desire to spread chaos and destruction would put both heroes in a difficult situation.
It could be someone like Doctor Octopus who gets his hands on some ninja technology. He could use it to enhance his mechanical arms and also start stealing chakra from people to power his new devices. His scientific mind combined with the newfound ninja powers would make him a formidable foe for Naruto and Spiderman.
The Joker could be a great main antagonist. Imagine he teams up with some of Spider - Man's foes like the Green Goblin. They could create a chaotic plan to take over both Gotham and New York. Their combined madness would be a huge threat to both Batman and Spider - Man.
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.
In this crossover fanfiction, Naruto would be a main character. Another important character could be Layla Williams from Sky High. Her power of telekinesis could interact in interesting ways with Naruto's jutsu. For example, they could combine their powers to defeat a common enemy. And of course, Naruto's friends like Sasuke or Sakura might also make appearances in the story, adding more depth to the interactions.
A powerful sorcerer who wants to harness the power of the earth and sky for his own selfish gains could be a great antagonist. He might try to corrupt the natural balance to gain unlimited power.
The Green Goblin could be a great main villain. He could be working on a plan that not only threatens Spider - Man's world but also the areas the Defenders protect. His maniacal nature and flying abilities would pose a great challenge to both Spider - Man's acrobatics and the Defenders' combat skills.
Another possibility is a corrupted dragon spirit that has been awakened due to the mixing of the two worlds. This spirit could be spreading chaos and trying to destroy both the ninja world and the dragon world. Naruto would have to figure out a way to stop it, as it has powers that are beyond what he has faced before.