In some fanfictions, it could be due to a genetic mutation or an unexpected side - effect of a jutsu he uses. For example, if he experiments with a new form of chakra manipulation, it might accidentally give him the power to summon swords. Or maybe it's a gift from the Sage of Six Paths in a different interpretation of the Naruto universe.
One possible origin could be some kind of ancient bloodline. Maybe Naruto has a hidden bloodline that was passed down through generations and finally awakened, allowing him to summon angels. Another option is that he got this ability through a special training or a quest. He might have found a hidden place or an old sage who taught him the art of summoning angels.
Perhaps it's related to his connection with the Nine - Tailed Fox. In the original Naruto story, he has a strong bond with the Nine - Tailed Fox. In the fanfic, this bond could have evolved in a way that allows him to summon foxes. It could be a manifestation of the latent power within him that he finally manages to tap into and use to summon these fox - like creatures.
It could be a result of some kind of rare genetic mutation. Maybe there was a dormant gene in his Uzumaki bloodline that got activated under certain circumstances, like during a near - death experience or a powerful chakra surge.
It could be from some sort of ancient ninja training that was lost and he somehow discovers it. Maybe there's a hidden scroll or a hermit who teaches him this fire - controlling ability.
One possibility is that he inherits it through some sort of bloodline connection that was previously unknown. Maybe there's a distant relative who had the ability to control sand, and it somehow got passed down to Naruto.
One possibility could be some sort of new training he undergoes. Maybe he discovers a hidden jutsu scroll that teaches him how to control and produce fire from within his body. This could be a long - lost technique from an ancient ninja clan.
Well, in some fanfictions, Naruto's water - controlling ability could be a gift from a powerful sage. This sage, seeing Naruto's potential and his need for new powers to face upcoming threats, bestows upon him the ability to control water. Another origin could be that Naruto accidentally absorbs the chakra of a water - using enemy during a battle, and this chakra somehow melds with his own, giving him the power to control water.
It could also be a result of a powerful curse or blessing. For instance, he might be cursed by an old enemy with the ability to control time as a side - effect, but he then learns to master it. Or, it could be a blessing from a sage or some other powerful being who sees Naruto's potential and gives him this unique ability to help him save the world.
It could be a result of some ancient jutsu that was passed down but lost in the main Naruto story. Maybe it was a power given to him by a mysterious entity to help him in his journey.
It could be the result of some kind of special training. Maybe he met a hermit who taught him a unique technique to perceive chakra in a visible way. For example, this hermit might have had him meditate in a special chakra - rich area and gradually opened his eyes to the world of visible chakra.