The Naruto universe has always struck me as a post-post-apocalyptic world: a great cataclysm wiped out much of the planet and it has been given plenty of time to regrow. The reason for this is because while the culture of the elemental nations appears to be very old by our standards, there are still quite a few snippets that prove that this is (or was) a modern world. When team seven is attempting to catch Tora the first time, they're using sleek, tiny, ear-mounted radio headsets, in the chuunin exam prelims a big-screen TV folds out of the wall, the hospital has computers at the nurses station, etc. However the elemental nations don't appear to have the population or technology base to support the manufacturing of these technological marvels. The explanation? Lost technology. Things that came from before.
If you look up the Rikudo Sennin, he brought the end of a great war by being the first to harness this new energy: Chakra. But what is chakra? What started the great war? My belief is that the war he ended is actually the tail-end of a greater war that has been going on for years and is what originally ravaged the planet: The Great Cape War. All of the heroes, villains, mutants, aliens, mages, and other assorted freaks that make up the Marvel universe finally couldn't work things out and started to throw down. After it started it just kept escalating and escalating and escalating until us normal humans couldn't stay to the side any longer.
Long story short: magic, nuclear radiation, and mutation add up to create what we now know of as nature chakra. Highly poisonous to "normal" life, the people, animals, and other life had to adapt to this new environmental hazard, just like it did to the toxic by-product of the first photosynthesis reaction: oxygen. Now, like oxygen, this formerly poisonous "chakra" is now required by almost all life on earth to exist. Channeling this chakra would have the unintended side-effect of unlocking and changing some mutations from the old world. A mutant's descendants would get a bastardized version of his power in addition to the benefits of chakra: these abilities would come to be known as Kekkei Genkai. For Example: The Sharingan is descended from Taskmaster's skill copying ability, the Inuzaka's bestial features and enhanced senses are courtesy of their ancestor Saber-tooth, the Kaguya clan's bone-manipulation is owed to the morlock: Marrow. I could list more all day, but that is not what this story is about.
This story is about two survivors. Two people who have lived through the flames of the old world and watched the new world spring up on its ashes. These two immortals have wandered the planet, watching humanity rise up from the grave they almost dug for themselves. Two mutants who have decided to return to a place they tried to call home for a while, so long ago. The last two humans without chakra look out over a ruined island surrounded by whirlpools: the grave of their descendants.
"Laura" He growled around an unlit cigar stub, "I'm gonna make a whole lotta heads roll for this."
She looked at her companion, the closest thing she had to a father. The anger in his eyes mirrored in her own. "I know, Logan. I know."
An in-depth background for a simple premise: Wolverine and X-23 in Konoha. By making Logan and Laura the ancestors of the Uzumaki (Not with each other! Jeez, that gives whole new meaning to the phrase "go f**k yourself") it gives them a legitimate reason to seek out the survivors of their extended family and try to protect them. Starting with Uzu's strongest former ally: Konoha.
Some more to consider:
The Uzumaki: enhanced lifespan, regenerative abilities, bottomless stamina.
Wolverine: spends a lot of time in Japan, has a thing for redheads.