That ship's weirdness is exactly what makes it interesting. It starts with the mentor angle from Part 1, which gets completely warped after the truth comes out. There's a whole subgenre of fics that treat the entire thing like a psychological thriller—Naruto, as an adult, trying to reconcile the ghost of this man who was both a villain and a savior. Some writers latch onto the shared Jinchuriki-adjacent trauma angle, the loneliness of bearing a huge power no one asked for. It's less fluffy romance and more about building trust from literal ashes. I've seen a few post-war stories where Itachi, having been reanimated and then stuck around somehow, has to face the living consequence of his plans: a Naruto who inherited the world he tried to save but in a way he never anticipated. The dynamic shifts from hunter/prey or mentor/student into two profoundly isolated people who might be the only ones who can truly get how heavy that 'savior' label really is, for better or worse.
A lot of the time, the fandom doesn't even write them in a traditional romantic context. It's more about the intense, obsessive, almost philosophical entanglement. Naruto's whole thing is about breaking cycles, and Itachi is the ultimate symbol of a cycle of sacrifice and failure. Putting them together forces both characters into this uncomfortable space where healing doesn't look like forgiveness, it looks like a very tense, quiet understanding. I remember one story that was just them talking in a safe house for 20 chapters, barely touching, and it was more gripping than any action scene. The themes aren't about love conquering all; they're about what it means to rebuild a self when your foundation is someone else's tragic legacy.