One possible way could be that he is experimented on by a rogue ninja or a secret organization. They might try to create a super - ninja by combining the powers of the Uzumaki and Uchiha clans, and as a result, Naruto ends up with a Sharingan in one eye. This would also lead to a lot of internal and external conflicts for Naruto as he tries to understand and control this new power.
Perhaps it's a gift from some ancient being or a prophecy. The Sharingan could be seen as a necessary tool for Naruto to face a greater threat that is coming. So, an entity gives him the power, but with it comes the burden of learning how to use it without being consumed by the dark side of the Sharingan's power.
In some fanfictions, he might obtain it through a powerful jutsu gone wrong that somehow fuses Uchiha DNA with his own. Maybe during a battle where he's exposed to some strange chakra energy related to the Sharingan.
One possibility could be through a forbidden jutsu experiment gone wrong. Maybe some rogue ninja was trying to create a super - powered being and Naruto ended up being the subject. The Sharingan was transplanted into him, but only one eye was successful.
Well, in some fanfictions, he might obtain it through a strange encounter. Maybe he stumbles upon an ancient relic during a mission that contains the power of the broken eye dojutsu and it somehow bonds with him.
In fanfiction, Naruto could get the Sharingan through a blood - related connection that is revealed later. For example, it could be discovered that he has some distant Uchiha ancestry that gets activated somehow. Maybe a powerful enemy's attack awakens this dormant Uchiha blood in him, and as a result, he develops the Sharingan. It could also be that a powerful sage or a new character uses their own unique powers to bestow the Sharingan upon Naruto for a specific purpose.
In some fanfictions, it could be through a special jutsu or ritual. Maybe Itachi, before his death, transferred his Sharingan to Naruto in a unique way, perhaps using a forbidden technique that was known only to a few in the Uchiha clan.
Well, in some fanfictions, he might inherit it from an unknown ninja clan. Maybe his parents left it for him and it was hidden until he discovers his true heritage.
Well, he might obtain it in a fight. Maybe after defeating an enemy who had stolen Zabuza's sword from its original place. Or perhaps he discovers it in an old, forgotten hideout where Zabuza once stashed his things.
In a fanfiction, Naruto might obtain the Rinnegan and Sharingan through a unique encounter. For example, he could stumble upon a dying Uchiha who transfers his Sharingan to Naruto in a moment of desperation. As for the Rinnegan, it could be related to his connection with the Sage of Six Paths. Perhaps the Sage's spirit, seeing the great need in the ninja world, bestows the Rinnegan upon Naruto. It could also be a result of some sort of genetic experimentation gone wrong but in a way that gives him these powerful eyes instead of harming him.
In fanfiction, Naruto could obtain the Golden Sharingan through a powerful ninja ritual. Maybe a sage or an ancient ninja figure passes on the power to him as a last resort to save the ninja world from a great evil. For example, if there's a threat that only the combined powers of the Uzumaki and Uchiha clans can defeat.
He might gain enhanced perception abilities, which would be a huge boost to his combat skills. With the Sharingan, he could predict his opponents' moves more accurately.
In fanfiction, it could be due to a strange encounter with a magical or ancient artifact. This artifact has the power to transfer the Sharingan's essence from Madara to Naruto. It might be a relic from an ancient battle between the Uchiha and some other powerful force, and when Naruto and Madara come into contact with it, the transfer occurs.