Okay, so the classic 'Harry has the Rinnegan' premise. I've seen a dozen ways writers tackle this. A big chunk of them go for the 'inheritance' route—somehow, a dormant Uchiha or Ōtsutsuki lineage surfaces in the Potter bloodline, maybe through a squib ancestor who traveled ages ago or some magical genetic experiment. It's a bit hand-wavy, but it lets the story jump right into the power fantasy.
Others prefer a fusion 'reincarnation' angle. Harry isn't just Harry; he's the soul of, say, Nagato or Madara reborn in the wizarding world. The Rinnegan manifests as his magic reacts to extreme stress, like the Dursleys' abuse or a near-death encounter with Voldemort. This often comes with traumatic memory flashes that drive the plot.
The methods I find more interesting are the ones that involve an artifact or a deliberate transfer. I read one where the Sorcerer's Stone wasn't just for immortality but was a condensed form of chakra, and absorbing its powers triggered the evolution. Another had a dying Sasuke, stranded from a dimensional rift, willingly passing his eyes to infant Harry as a last act, binding their fates. Those setups usually lead to more intricate plots than just 'Harry suddenly has god-like eyes.'
Honestly, the how is less important than what the writer does with it afterwards. Does it make him isolated, feared? Does Dumbledore see it as a dark artifact? That's where the real story usually lives, or dies.