One possible plot could be that Naruto is somehow transported to the Spider - Man universe. Maybe he lands in New York and is mistaken for a new kind of super - powered being. Spider - Man, being curious, approaches him. Naruto, not understanding this new world, starts using his ninja skills which amaze the people around. They then team up to fight a common enemy like the Green Goblin who has somehow got hold of some chakra - based technology. The combination of Naruto's ninjutsu and Spider - Man's web - slinging and super strength would make for an epic battle.
The plot might involve a villain who is trying to merge the two worlds for his own evil purposes. This villain discovers a way to open portals between the Naruto universe and the Ultimate Spider - Man universe. Naruto and Spider - Man are both drawn into this mess. They have to learn about each other's powers and worlds quickly in order to stop the villain. For example, Naruto could teach Spider - Man some basic ninja stealth techniques, and Spider - Man could show Naruto how to use the city's infrastructure to his advantage during a fight. Along the way, they also form an unlikely friendship.
Another possibility is that some sort of cosmic event makes them both super - charged, Naruto becoming godlike and Spider - Man reaching an ultimate form. They are then chosen to stop an interdimensional threat that could destroy both their worlds. They would have to learn to trust each other quickly and use their combined powers to save the day.
One idea could be a crossover with the X - Men. Spider - Man could find himself in the middle of a conflict between mutants and anti - mutant forces. He'd have to use his quick thinking and agility to help the X - Men protect the young mutants. Another could be a crossover with the Fantastic Four. Maybe Spider - Man gets caught in one of Reed Richards' experiments gone wrong and they all have to work together to fix it while also dealing with a new super - villain that emerges from the chaos.
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.
If it's a crossover with the Fantastic Four, perhaps a cosmic entity is attacking Earth. Spider Man teams up with them to stop it. But during the battle, he's exposed to some deadly radiation from the entity. Despite the Fantastic Four's efforts to save him, his body can't withstand it, and he dies. His death could lead to the Fantastic Four creating new safety protocols for future battles.
Maybe he fakes his death to protect his loved ones from a powerful enemy. He could be trying to draw out a villain who has been targeting his family and friends.
In an 'ultimate spider man crossover fanfic', a really interesting crossover could be with Venom. But instead of being enemies, they team up. Maybe there's a new symbiote - like threat that is even more powerful and they have to combine their powers to defeat it. Another idea is a crossover with the Guardians of the Galaxy. Spider - Man gets accidentally transported into space and has to team up with Star - Lord and the gang to get back home while also fighting off some space - pirates.
If Naruto were in Ultimate Spider - Man fanfiction, it could be amazing. Naruto is known for his determination and never - give - up attitude. He could inspire Spider - Man in different ways. Also, his unique fighting style would be a contrast to Spider - Man's web - slinging and acrobatics. Maybe they would have some friendly competitions to see who's better at what, while also working together to keep the city safe.
One possible plot could be that Spider - Man and Wonder Woman team up to stop a powerful villain who has the ability to manipulate time. Spider - Man's agility and quick thinking combined with Wonder Woman's strength and magical weapons would make for an exciting adventure. They might start off not trusting each other fully, but as they face challenges together, they learn to work as a team.
One possible plot could be that Spider - Man gets accidentally transported to the Avengers' headquarters. He has to prove himself to the Avengers at first, since they don't really know him well. Then, they discover a common enemy that is planning to attack both New York City (Spider - Man's territory) and other major cities around the world that the Avengers protect. Together, they combine their powers and skills. Spider - Man's agility and spider - sense work well with Iron Man's technology, Captain America's leadership and combat skills, Thor's godly strength, etc. They have to overcome their differences in fighting styles and strategies to defeat the enemy.