Naruto would probably be very curious about Ms Marvel's powers. He might ask her a lot of questions and be excited to see her in action. Ms Marvel, on the other hand, would be intrigued by Naruto's ninja techniques. They would likely start by showing off their abilities to each other.
One possible plot could be that Naruto and Ms Marvel are brought together by some sort of interdimensional rift. Naruto, with his ninja skills, and Ms Marvel, with her superpowers, have to team up to close the rift. They start off not understanding each other's worlds but gradually learn to work together. For example, Naruto could teach Ms Marvel about stealth and chakra, while she could show him how to use her powers in different ways.
One interesting crossover could be Naruto teaching Ms Marvel some of his ninja skills, like tree - walking. Since Ms Marvel has super strength and agility, she might pick up these skills quickly. This could lead to a new adventure where they face a common enemy together.
There could be many interesting plotlines in such a fanfiction. Maybe it could start with a strange accident that leads to Ms Marvel becoming pregnant with Peter Parker's child. For example, some sort of magical or scientific experiment gone wrong. Their relationship would then be tested as they deal with the challenges of an unexpected pregnancy. They would have to face the reactions of their friends and families, like Peter's Aunt May and Ms Marvel's own family. Also, they would need to figure out how to balance their superhero duties with the impending parenthood.
Definitely not. Ms. Marvel's powers weren't a result of being a mutant. Instead, her powers were attributed to unique circumstances or incidents within the comic's narrative.