I'm not sure specifically as there could be many different plots for such a fanfic. It might involve Naruto characters being transported to the X - Men world or vice versa, and then they have to deal with the different powers, cultures and challenges in that new world.
The plot could involve Naruto characters being transported to the X - Men world or vice versa. They might team up to face a common threat that is affecting both worlds, like a powerful villain who is stealing chakra and mutant powers. Maybe Naruto and Wolverine could bond over their shared experiences of having a power within them that they have to constantly control.
Definitely Naruto from the Naruto series. And from the X - Men, characters like Wolverine or Professor X are very likely to be main characters as they are some of the most well - known X - Men.
I think Naruto and Rogue would be an interesting pairing. Naruto has a strong will and positive energy, and Rogue is always worried about her power harming others. Naruto could perhaps help Rogue gain more confidence in herself and her abilities. Also, his chakra might interact in an unexpected way with Rogue's power - absorption ability.
It could be about Naruto existing in two different realms or having to navigate between two contrasting aspects of his world. Maybe it's about his life as a ninja and his inner self which are like two separate worlds.
One possible plot could be that Naruto is on a mission in his world and gets caught in a powerful jutsu that sends him to the X - Men's universe. There, he's in danger as he doesn't understand this new world. Rogue senses his distress and saves him from some immediate threats like angry mobs who are scared of his strange appearance. Then they start to communicate, with Naruto trying to explain his situation using hand signs and simple words, and Rogue trying to understand and help him get back home.
Well, you could start by having a common villain. For example, the Green Goblin could team up with a mutant - hating group. This would force Spiderman and the X - Men to work together. Spiderman might be initially against the X - Men because he's not used to their way of doing things, but as they face the common threat, they start to understand each other.
One possible plot could be that Naruto is somehow transported to the X - Men universe. He teams up with Wolverine. Naruto's unique ninja skills, like his shadow clones, could be used in combat against the Brotherhood of Mutants. Wolverine could teach Naruto about the concept of mutants and their struggles, and Naruto could in turn show Wolverine some of his ninja wisdom.
One interesting plot could be that Naruto is somehow transported to the X - Men universe. He teams up with Wolverine. Naruto's ability to create shadow clones could be used in interesting ways during battles, like confusing the enemies. Wolverine could teach Naruto some combat skills from the X - Men's fighting style. They could go on a mission to stop a powerful mutant villain who has plans to take over the world, using Naruto's chakra powers and Wolverine's adamantium claws.
In a Ben 10 and Naruto fanfic, their powers would be a great combination. Ben has the ability to transform into various alien forms, each with unique powers. Naruto has his chakra and his powerful jutsu. They could learn from each other. For example, Ben could teach Naruto about some of the alien technologies, while Naruto could teach Ben about chakra control and the ninja way.
One way their worlds could collide is through a cross - dimensional rift. Maybe Naruto is on a mission and accidentally gets sucked into the X - Men's universe. Rogue, being the curious and empathetic character she is, might be the first to approach Naruto. She could be intrigued by his unique chakra powers. Naruto, on the other hand, would be completely bewildered by this new world full of mutants with strange abilities.