Man, it's wild how many directions writers take that prompt. There's a hefty backlog out there, and honestly a lot of it melts together into generic 'OP-Naruto-with-daddy-issues' territory. I got hooked on one called 'Kurosaki' where he's actually raised as a Quincy in the 'Bleach' universe after the Fourth Hokage made some desperate deal. It's less about flashy power-ups and more about him navigating the spiritual politics of Soul Society, trying to hide his chakra nature, and the sheer awkwardness of having Isshin as a stand-in dad. The pacing is glacial sometimes, but the world-building feels earned.
A lot of people recommend 'Son of the Sannin' but that's a totally different beast—more about Jiraiya finding him post-Kyuubi and the Yami part is treated as a latent curse mark-like entity he has to suppress. It's well-written but barely touches the crossover element you're probably looking for. The one that nailed the dark, atmospheric tone for me was a deadfic called 'Shadows in the Leaf.' It died years ago, but the first ten chapters are a masterclass in tension—Naruto's chakra is literally corrosive, harming anyone he tries to get close to, and the Yami heritage is portrayed as a sickness the village fears rather than a cool power. I'm still bitter it never finished.