The main antagonist could be a powerful and corrupt shinobi from within Konoha itself. This person is jealous of Naruto's popularity and power. They plot against him and manage to get him in a situation where he loses his left eye. They then try to frame Naruto for various crimes to further isolate him from the village, while Naruto has to prove his innocence and also deal with his new disability.
Perhaps the main antagonist is an ancient demon that has been awakened. This demon's power is so great that it manages to injure Naruto and take his left eye. The demon could be after the Nine - Tails' chakra and sees Naruto as an obstacle. It would constantly be hunting Naruto down, forcing him to become stronger and find ways to fight back without the full use of his vision.
It could be a rogue ninja from a hidden village that has a grudge against Naruto. This ninja might have a special jutsu that specifically targets Naruto's left eye during a fight, causing him to lose it.
It could be a new, mysterious ninja from a far - off land. This ninja might have a vendetta against Naruto for some reason, like Naruto interfering in their plans before. They could be extremely powerful and use some sort of dark jutsu to target Naruto's eye specifically.
It could be a power - hungry warlord in the story's setting. This warlord might be the one who ordered an attack on Carl's group, leading to Carl losing his eye.
It could be an old enemy like Kronos. Kronos is extremely powerful and cruel. He might target Percy's eye as a way to weaken him both physically and mentally. By taking away Percy's eye, Kronos hopes to make Percy less effective in battle and to shatter his confidence, which is crucial for leading the demigods against him.
In this fanfiction, it could be that Naruto's left - eye loss is part of a curse placed on him by an ancient evil. This curse not only takes his eye but also starts to drain his chakra. Naruto then has to search for the origin of the curse to break it. Along the way, he meets some new characters who either help or hinder him. His relationship with Sasuke could also be affected as Sasuke might see Naruto as weakened and try to protect him in his own way, which Naruto would initially resist as he doesn't want to be seen as a liability.
It could be Orochimaru. He's always been interested in Naruto's power. Maybe he devises a plan to make Naruto lose his memory so he can manipulate him more easily, perhaps to use him as a weapon against the Hidden Leaf.
It could be Kaguya. If Kaguya were to return and use her powerful abilities to drive Naruto mad, perhaps by invading his mind with dark thoughts and memories. She has the power to warp reality and minds, so she could easily make Naruto lose his sanity. And since she has a grudge against the world of ninjas, making Naruto, one of the most powerful ninjas, go insane would be a great way for her to start her reign of terror all over again.
A new and mysterious dark ninja could be the main antagonist. This character might have a special ability to corrupt others. They target Naruto specifically because of his power and influence. By using some form of dark jutsu or psychological manipulation, they make Naruto lose his humanity, turning him into a weapon against the very people he used to protect.
The Akatsuki could be the main antagonists. They might think that Naruto's voice holds some key to a powerful weapon or secret. So they send one of their members, like Zetsu, to steal Naruto's voice. Zetsu's ability to blend in would make it easier for him to get close to Naruto and carry out the deed.
It could be a new, powerful ninja from a hidden village. This ninja has a special ability to manipulate the chakra related to emotions. He sees Naruto as a threat because of his popularity and power, so he uses his ability to make Naruto lose his emotions, hoping to weaken him and his influence.
It could be a new and powerful rogue ninja who manages to overpower Naruto and cause him to lose his arm. Maybe this antagonist has some sort of vendetta against Naruto or the Hidden Leaf village.