Maybe it could be through some sort of magical jutsu. Naruto is known for his unique ninjutsu skills in his own universe. He might have developed a new jutsu that allows him to connect with and control the Hulk's mind. For example, it could be a jutsu that detects and manipulates gamma radiation, which is what created the Hulk. Or perhaps he found a way to use his chakra in a new way to interface with the Hulk's rage - powered form.
Well, it might be due to a crossover of universes' rules. In Naruto's world, chakra is the fundamental power. But in the Hulk's world, gamma radiation is key. In the fanfiction, perhaps there was an event that made these two powers interact in a way that Naruto could control the Hulk. It could be a freak accident during a battle or an experiment gone wrong that merged their power sources in Naruto's body, allowing him to exert control over the Hulk.
It could also have implications for the Hulk himself. Usually, the Hulk is a wild and uncontrollable force. But with Naruto in control, he might be able to be used in more positive ways. The Hulk could be directed to help rebuild instead of just destroy. And from a character development perspective, the Hulk might learn to control his rage better under Naruto's influence, and Naruto might learn new things about power and responsibility from having to control such a powerful being.
Another possibility is that Naruto acquires the ability to control the weather from a powerful artifact. He might stumble upon an ancient relic during one of his adventures. This artifact has the power to control the weather, and once Naruto touches it or figures out how to use it, he gains this extraordinary ability. It could be that the artifact was created by a long - forgotten civilization that had mastered the art of weather manipulation.
Maybe it could be due to some dark jutsu he discovers accidentally. For example, he might find an ancient scroll in a hidden cave that details the method of controlling corpses. This could be a jutsu forgotten by time, and Naruto, being the curious and determined ninja he is, decides to study it.
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.
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.
Sometimes he can, but it depends on the situation and the storyline. Usually, it's a struggle for him.
He might gain it through a series of trials. Maybe he has to face his deepest fears in some kind of mental realm where the Kyuubi resides.