He could find it during one of his adventures. Maybe he's exploring a new land or a hidden cave and stumbles upon the Tesseract. It could be that the Tesseract was brought to his world by some kind of interdimensional traveler and Naruto just happens to be the one to discover it.
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.
Well, in some fanfictions, Naruto might gain the ability to control nature through intense training with a hermit or some ancient spirit. For example, he could be led to a hidden grove where the essence of nature is concentrated, and by communing with it over time, he gradually unlocks the power to control nature.
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.
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 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.
It could be through some kind of ancient training method. Maybe he discovers a hidden scroll that details the art of blood control and spends months or even years mastering it.
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.
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.