In some fanfics, it could be due to a forbidden jutsu he discovers. Maybe he stumbles upon an ancient scroll that details the process of controlling the dead.
Another possibility is that it is related to his own unique chakra. Naruto has always had an extraordinary amount of chakra, and perhaps in the fanfic, some kind of mutation or evolution of his chakra gives him the ability to control the dead. This could be triggered by a near - death experience or a strong emotional event that causes his chakra to react in an unexpected way.
In some fanfiction concepts, it could be due to a new, powerful jutsu he discovers or perhaps as a result of some ancient curse or blessing that is bestowed upon him.
In some fanfictions, Naruto might gain the ability to control iron through special training with a unique jutsu master. This master could teach him how to manipulate the iron elements in the environment using his chakra in a very specific way.
In some fanfictions, Naruto might gain the ability to control the weather through a special training. Maybe he discovers a hidden jutsu or power within himself during a difficult mission or in a secret place. For example, he could find an ancient scroll that teaches him weather - controlling techniques.
Another way could be as a result of a special encounter. Maybe he discovers a hidden scroll or a mysterious artifact that imparts the power of lightning control to him. This discovery could be accidental, like when he's exploring an ancient ruin or during a battle when he stumbles upon something unexpected.
In some fanfictions, Naruto might gain the ability to control the flood through a special training with a hermit who has water - based powers. This hermit could teach Naruto unique jutsu related to water manipulation on a large scale.
In some fanfictions, it could be related to an ancient bloodline limit that was dormant in Naruto all along. His Uzumaki heritage might have some connection to water - related powers, and through some sort of emotional or physical trigger, he is able to access and control the ocean.
One consequence could be that it disturbs the balance of the ninja world. The dead are supposed to rest, and by controlling them, Naruto might be messing with the natural order. This could lead to other ninja clans or villages seeing him as a threat.
Well, it could be that Naruto's own chakra nature evolves in an extreme way. His Uzumaki bloodline might have some hidden potential that, when combined with his experiences and growth as a ninja, mutates into the ability to control black holes. For example, his chakra, which is already very powerful, could reach a new level where it can warp space to form black holes.
There could be a situation where an ancient technique is awakened within Hinata. This technique might have been long forgotten, but due to certain events in the fanfiction world, it resurfaces. This ancient technique could be the key to her being able to control Naruto's seal. It might involve her chakra nature or some spiritual connection she has with the seal's origin or the entity that placed the seal on Naruto in the first place.
His blood control ability might also create new alliances or enemies. Allies could see his power as a great asset and join him, while enemies might fear his newfound ability and target him more aggressively. In the context of the fanfic, this would add more twists and turns to the plot. Maybe some characters who were neutral before would now side with Naruto because of his blood control, or some of his old enemies would form stronger alliances against him.