Perhaps it was a sacrifice. Naruto might have given up one of his eyes voluntarily to save someone. Maybe to save Sasuke from a genjutsu that was slowly consuming his mind, and Naruto's eye was the key to breaking the genjutsu.
It could be due to a battle injury. Maybe he got into a really tough fight with a powerful enemy, and in the process, lost an eye. For instance, a fight against a rogue Akatsuki member who has a very dangerous eye - related jutsu.
There's also the possibility that it's an accidental injury caused by one of Naruto's friends during a training session gone wrong. For example, Sasuke could accidentally unleash a jutsu that hits Naruto's eye while they are sparring.
This change in Naruto having one eye could lead to a whole new character arc. Maybe he'd be more self - conscious about his appearance, which could affect his relationships. He might also develop new jutsu that are more suitable for his one - eyed state, like a jutsu that uses his remaining eye's chakra in a more focused way.
It might be due to some sort of bloodline fusion. Naruto is known for his Uzumaki heritage, but perhaps there was an unexpected encounter with another clan's power that merged with his own, and as a result, one of his eyes turned red as a new and unique ability emerged.
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.
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.
The third eye might have the power of long - distance vision. Naruto could use it to spy on enemy camps or look for missing comrades from afar. This would be a useful addition to his skills, especially when planning strategies or rescuing hostages. He could also use it to keep an eye on the Akatsuki's movements across different regions without having to be physically close.
He could potentially create a jutsu that combines the Rasengan with the Byakugan's ability to see chakra points. For example, he could create a Rasengan that specifically targets an enemy's chakra points, making it a more lethal and precise attack. Maybe he could call it the Byakugan - Rasengan. Another possibility is a jutsu that uses the Byakugan's long - range vision to track an enemy's movements and then sends out a series of shadow clones that are guided by that vision to surround and attack the enemy.
If Naruto had a third eye in fanfiction, it could greatly enhance his perception abilities. He might be able to detect hidden enemies or traps more easily. For example, in battles, he could see chakra movements from all directions without having to rely so much on his regular senses. This could make him even more formidable in combat and change the dynamics of his fights against powerful foes like Sasuke or Pain.
He could have enhanced vision powers, like seeing through illusions more easily or being able to detect chakra signatures from a much greater distance. The red eye might act as a sort of sensor, similar to how the Byakugan can detect things, but with its own unique properties.
Perhaps it's a dojutsu that can manipulate the elements in a new way. For instance, it could turn his wind - style jutsu into something more powerful and less predictable. It might also have the ability to absorb the chakra of his opponents when he makes eye contact with them, which would give him an edge in battle. The appearance of the dojutsu could be something like a swirling pattern in his eye.