It could be a combined form of several of Spider - Man's classic villains. For instance, Doc Ock, Electro, and Sandman fused together by some dark magic. This new super - villain would have the intelligence of Doc Ock, the electrical powers of Electro, and the shape - shifting abilities of Sandman. Spider - Man would have to use all of his skills and perhaps some new ones he gains during the crossover to defeat this powerful adversary.
In a Spider Man Destiny Crossover Fanfic, perhaps Spider - Man crosses paths with characters from other superhero franchises. For example, he could end up in the world of the X - Men and have to work with Wolverine and Storm to stop a mutant - hating villain from destroying both the mutant and human worlds. He might learn new skills from the X - Men and bring them back to his own world.
The Green Goblin could be a great main villain in a crossover. Imagine if he teams up with Doctor Doom from the Fantastic Four universe. Their combined evil intelligence and power would be a huge threat to Spider - Man and whoever he teams up with in the crossover.
It could be Doctor Doom. He might be seeking to take over multiple universes in a crossover. Spider Man stands in his way, and Doom, with his superior intellect and powerful magic, manages to defeat Spider Man. His death would then be a huge shock to other heroes in the crossover, like the Avengers or the Fantastic Four who then have to avenge him.
It could be Loki. He's always causing trouble for the Avengers. He might see kidnapping a fan as a way to mess with Spider - Man and the Avengers, since he enjoys chaos and manipulation.
Venom is also a strong candidate. In this fanfiction, he could be more powerful than ever. He might be infected with some sort of alien symbiote that gives him enhanced abilities. Venom could target Spider - Man because he wants to prove that he is the stronger one. And by attacking Spider - Man, he also draws the attention of the Avengers, which he sees as a challenge. He could start by attacking the city and luring Spider - Man and the Avengers into a trap.
How about a new villain created specifically for the fanfiction? A being made up of the combined negative energy from all the spider - verses. This entity could be called the 'Void - Spider' and it feeds on the chaos and destruction that often follows Spider - Man in his battles. It would be a very powerful and unique threat that the Spider - Men from different universes would have to face together.
Dr. Octopus could be a great main antagonist. He could team up with a female super - villain from the Totally Spies universe. Together, they could create a plan to steal some top - secret technology. Dr. Octopus uses his mechanical arms to cause chaos in the city, while the female villain uses her own unique powers to keep the Totally Spies and Spider - Man at bay.
The Kingpin might be a good choice. He could see the Titans as a new weapon to use in his criminal empire. He could form an alliance with some of the more corrupt elements in the Attack on Titan world, like some of the military commanders who are only interested in power. He would use his wealth and influence to control the Titans and try to take over both universes. Spider - Man and the heroes from Attack on Titan would have to fight against his well - organized and well - funded forces.
The Green Goblin is one of the main villains. He has his own set of powers and is always causing chaos in Spider Man's city.
For a more unexpected choice, you could have the Arbiter from Halo as one of the main characters. He has a complex backstory and his own code of honor. In a crossover, he could team up with a Hunter Guardian. The Hunter's brute strength combined with the Arbiter's strategic thinking would make for an exciting story as they face challenges in both universes.