Well, one type of villain they could face is a powerful sorcerer. This sorcerer could be casting dark spells all over the city, turning people into stone or creating dangerous illusions. Spider - Man might be able to use his agility to avoid the illusions and find the source of the magic, while Supergirl uses her super strength to break the stone - like prisons of the people. Another villain could be a bio - engineered monster with super strength and the ability to regenerate. Spider - Man and Supergirl would have to figure out a way to stop its regeneration, perhaps by finding a weak spot together.
A really cool villain for them to face together could be a shape - shifter. This shape - shifter could take on the forms of their loved ones to trick them. But Spider - Man's spider - sense would give him a hint that something is wrong, and Supergirl's X - ray vision could help them figure out the real identity of the shape - shifter. Also, a villain with the power to control the weather on a global scale would be a great challenge. Supergirl could try to counter the extreme weather conditions, while Spider - Man swings around to rescue people in danger.
They could face a villain who has the power to control technology, like a super - hacker. This villain could use his skills to disrupt the city's infrastructure, and Naruto and Spiderman would have to use their combined skills to stop him. Naruto could use his ninjutsu to physically take on the villain while Spiderman uses his web - slinging and acrobatics to dodge the villain's technological attacks.
The Lizard could be turned into a more supernatural villain. Maybe he gets possessed by an ancient spirit that makes him not only stronger but also able to control other reptiles with dark magic. This would pose a huge threat to Spider - Man as he has to deal with the Lizard's new powers on top of his already dangerous physical abilities.
Another idea is that there's some sort of interdimensional rift that brings Supergirl to Spider - man's world. At first, they might be a bit suspicious of each other, but then they realize they have a lot in common. They could start sharing their stories and then work together to find a way to send Supergirl back to her own dimension while also dealing with any local threats in Spider - man's city.
Well, their team - up would be amazing. Spider - Man's acrobatic skills and web - slinging along with Supergirl's super strength and flight could make for some really cool action scenes. They could fight villains that neither could handle alone. For example, a powerful alien who can resist Spider - Man's physical attacks but is vulnerable to Supergirl's heat vision, and at the same time, Supergirl might need Spider - Man's quick thinking and agility to deal with the villain's minions.
She might face the challenge of intangibility. Ghosts can be intangible, making it hard for Supergirl to land a physical blow.
Another adventure could be exploring some ancient ruins that hold a powerful but dangerous energy source. Iron Man's technology could help them navigate and analyze the ruins, while Spider - Man's spider - sense could keep them safe from any hidden traps. They'd have to work together to either contain or utilize the energy source without causing chaos.
Well, the Kingpin could be a main villain. He could see Naruto as a threat to his criminal empire in New York. He might hire some ninja mercenaries from the Naruto universe to take him down. And then there's Electro, who could be enhanced by some sort of chakra - based technology. He could use his new powers to cause chaos in the city and target Naruto specifically, thinking that he's the key to getting even more power.
Well, in a Spider - Man Flash crossover fanfiction, there could be an epic race between the two. The Flash could be testing his speed against Spider - Man's agility and web - slinging skills. Maybe they start as rivals but end up teaming up to face a common enemy like a super - fast villain that only their combined powers can defeat.
One possible plot could be that they team up to stop a powerful villain who has the ability to travel between their two cities. Maybe this villain is stealing tech from Gotham and super - powers from New York. They start off not trusting each other as they have different methods. Nightwing is more stealthy and trained in combat, while Spider - Man is more quippy and uses his webs in a very acrobatic way. But as they face challenges together, they learn to work as a team and combine their skills to take down the bad guy.
One possible plot could be that Spider - Man gets transported to the RWBY universe. He might initially be confused by the Grimm and the Huntsmen and Huntresses. Maybe he teams up with Team RWBY to fight a new type of threat that combines the technology - based villains from his world and the Grimm from RWBY. For example, a villain could be using some sort of Dust - powered tech to create super - Grimm. Spider - Man's agility and web - slinging abilities would be a great addition to the RWBY team's combat styles.