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.
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.
The plot might involve a crossover of the two worlds' villains. For example, the Volturi from Twilight could team up with some of the super - villains in Sky High. The students at Sky High would then have to face this powerful alliance. They could use the unique abilities of the Twilight characters, like the werewolves' strength and speed, to help them in the fight. It would be a battle of different powers and strategies.
In a Naruto and Spiderman crossover, it could start with Spiderman noticing some strange energy signatures in his city. These turn out to be Naruto's chakra flares. Naruto is there looking for a way back to his own world after being accidentally sent to Earth - 616 (the Marvel Universe). They meet and at first don't understand each other. However, when they see a common enemy, a group of ninjas - like mutants who are causing chaos, they decide to work together. Spiderman uses his agility and web - shooting while Naruto uses his jutsu to defeat the bad guys.
A possible plot is that the RWBY characters end up in New York. Ruby, with her speed and scythe skills, is initially mistaken for a threat by Spiderman. But when they realize they are both on the side of good, they join forces. Weiss could use her glyphs in new and creative ways in the urban environment, Blake's stealth and acrobatic skills could be put to great use, and Yang's strength would be a valuable asset. Together they take on a criminal organization that has somehow gotten hold of some Dust and is using it for evil purposes.
One possible plot could be that a new super - villain emerges who has the ability to manipulate time and space. This brings the universes of Spiderman and Batman together. Spiderman's agility and sense of humor contrast with Batman's brooding and detective skills as they team up to stop the villain from collapsing both their worlds.
Maybe Naruto and Spiderman cross paths when a powerful ninjutsu experiment goes wrong and creates a portal between their two worlds. They initially misunderstand each other but then realize they have a shared goal of protecting the innocent. Together, they could combine their skills. For example, Naruto could use his shadow clones to create diversions while Spiderman sneaks up on the bad guys. And Naruto would be fascinated by all the high - tech gadgets Spiderman has.
One possible plot could be that the Big Hero 6 team is working on a new project in San Fransokyo when a strange series of crimes start to occur. These crimes seem to involve some sort of advanced technology that is out of this world. Spider - Man, who is on a school trip to San Fransokyo, senses that something is wrong. He starts to investigate on his own. Eventually, he crosses paths with the Big Hero 6. At first, there's some misunderstanding and a bit of a scuffle as they don't know each other. But when they realize they are after the same bad guys, they team up. Hiro figures out a way to integrate some of Spider - Man's web - slinging tech into Baymax's systems for a new attack mode, and together they take on the villain who is trying to use the stolen tech to create a portal to another dimension.
Maybe there's a powerful ancient artifact that has been stolen and is being used for evil purposes. This artifact has the power to disrupt the balance between different realms. Spiderman discovers some strange happenings in the city related to the artifact's power, like buildings randomly changing shape. Wonder Woman is also on the hunt for the artifact as it was stolen from a place under her protection. When they meet, Spiderman is initially in awe of Wonder Woman's strength and beauty. They team up, with Spiderman using his acrobatic skills to navigate through dangerous traps set up by the villains protecting the artifact, and Wonder Woman using her lasso of truth to find out where the artifact is hidden.
One idea could be that Spiderman gets transported to the Young Justice universe. He teams up with the team to stop a common enemy like Vandal Savage, who has some new high - tech weaponry. Spiderman's unique abilities like web - slinging and his spider - sense would add a new dynamic to the team's combat strategies.
One possible plot could be that Batman and Spider - Man both find themselves in Gotham City dealing with a new super - villain who has the ability to create illusions. Batman uses his detective skills to try and figure out the villain's true identity while Spider - Man uses his agility and spider - sense to fight the minions. They initially clash due to their different methods but then realize they need to work together to stop the big bad.