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.
Well, it could be that Naruto is bestowed with this power by some kind of magical being. Like, a spirit of the elements decides to give him the power to control the weather in order to help him protect the village. This would be a more fantastical way of him getting the ability.
Another possibility is that Naruto's strong emotions and his connection to the chakra of nature allow him to gradually develop the ability to control the weather. His will to protect his friends and the village might be so strong that it awakens this power within him. He has always had a special bond with nature, and this could be an extension of that.
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.
He could use it for defense. For instance, creating a huge storm to block enemy attacks or a thick fog to hide his village from invaders.
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.
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.
Well, perhaps he first notices it during a really intense storm at Hogwarts. Maybe he's out in the courtyard and suddenly the wind starts to change direction as he gets a strange feeling inside. It could be that he was in a Quidditch match and the clouds above started to move in an odd way when he was concentrating hard on winning.
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.