Naruto's ability to create shadow clones could combine with a mutant's telepathy. For example, he could send his clones to different locations and the telepathic mutant could communicate with each of them simultaneously, gathering information from all over. This would be a great way to gather intelligence or set up strategic attacks.
A really cool twist could be that Naruto's tailed beasts are actually ancient mutants that were sealed away long ago. When they start to emerge in the X - Men universe, they bring with them a new form of power that no one has ever seen before. This could create a power struggle between those who want to use the tailed beasts' power for good and those who want to use it for evil.
Obviously Naruto himself is a central character. His popularity from the original series brings a lot of attention. Then there might be characters from the crossover world that gain popularity. For example, if it's a crossover with a Final Fantasy world, characters like Cloud or Squall might be popular in the fanfiction.
There could be a really interesting fanfiction where Naruto characters possess immortal souls like in Soul Eater. For example, Naruto's strong will could be translated into an extremely powerful and unbreakable immortal soul. The ninja world's chakra system might interact with the concept of souls from Soul Eater in unique ways, like using chakra to enhance or protect the soul. Maybe Sasuke's Sharingan could have a new ability related to seeing and manipulating the immortal souls.
One common theme is the exploration of power dynamics. When the X - Men cross over with other groups, like the Avengers or the Fantastic Four, there's always a comparison and contrast of their powers. For example, in a crossover with the Avengers, the mutants' powers might be seen as more unpredictable compared to the technology - based powers of some Avengers.
One potential crossover character could be Harry Potter. Imagine Naruto, with his immortality, meeting Harry in the wizarding world. Naruto could teach Harry some ninja skills, and they could fight together against Voldemort. Another could be Superman. The contrast between Superman's superpowers and Naruto's ninja skills, along with Naruto's immortality, would make for an interesting story.
Well, one way it could work is by having Naruto's chakra system somehow be translated into the nen system of Hunter x Hunter. Naruto's immortality could be related to some sort of nen ability he discovers in the Hunter x Hunter world. Maybe his god - like powers would make him a target for certain groups in the Hunter x Hunter universe, like the Phantom Troupe. They might see his power as a threat or something they can use for their own gain.
One idea could be that Jinx somehow gets transported to the Naruto universe. She might initially be seen as a strange and powerful figure. Naruto, being the curious and friendly type, would approach her. Jinx could then start causing chaos in the Hidden Leaf Village, which Naruto has to deal with while also trying to understand her. And they could gradually form an unlikely friendship as they learn from each other's worlds.
A different approach could be that characters from the Matrix world are brought into the Naruto universe. Trinity could learn some ninja techniques from the Konoha ninja. The Matrix characters would be amazed at the concept of chakra and how it can be used for various powers, like walking on walls or creating fireballs.
Goku from Dragon Ball could be a great crossover character. His Saiyan powers and love for combat could contrast and interact in an interesting way with Naruto's ninja skills and immortal sage abilities. They could have epic battles or team up against a common enemy.