Perhaps in the fanfiction, Naruto is exposed to some sort of other - dimensional energy. This energy could be from a parallel universe or a different realm. His body and spirit, being as resilient as they are, adapt to this energy and he discovers that he can use it to control black holes. It could also be related to his willpower. Naruto's unwavering will to protect his friends and village might be the catalyst that unlocks this extraordinary ability.
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.
One possibility in this fanfiction is that Naruto is exposed to a powerful and otherworldly energy source. This energy could be from a different dimension or a long - forgotten relic. When he comes into contact with it, his body absorbs and adapts to it in a way that allows him to control black fire. This new power also comes with its own set of challenges and responsibilities for Naruto as he tries to integrate it into his existing set of skills.
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.
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.
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.
In some fanfictions, it could be due to a new jutsu he discovers. Maybe during a secret training session in an ancient scroll, he finds a forbidden technique that allows him to control people.