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.
The main antagonist could be an old enemy who has resurfaced and is more powerful than ever. This enemy targets Naruto specifically and manages to injure him so severely that he loses his arm. For example, Orochimaru could return with new and more deadly powers.
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, 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.
A possible main antagonist in such a fanfic could be a dark entity that has possessed someone close to Naruto. This entity could be using the host's body to get close to Naruto and then attacks him, resulting in the loss of his arm. Naruto would then have to figure out not only how to deal with his injury but also how to save his friend from the dark entity's control.
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 Voldemort, even if he's already been defeated in the original story. His lingering influence might still haunt Harry. Maybe there are some dark magic remnants of Voldemort that keep causing problems and making Harry feel hopeless.
It could be Zuko if the fanfiction takes a different turn. Maybe Zuko, still struggling with his own inner demons, sees Aang's loss of control as an opportunity to take advantage and gain power. So he tries to manipulate the situation to his benefit.