Perhaps an Orochimaru - like figure. Someone who is obsessed with power and experimentation. He may have heard rumors about some unique power in Naruto's eyes and decides to steal them for his own dark research. This antagonist would be highly intelligent and elusive, making it difficult for Naruto and his friends to track him down.
It could be a member of a long - forgotten clan that has a vendetta against the Uzumaki clan. They might believe that Naruto's eyes hold the key to their clan's downfall or revival, so they steal his eyes in an attempt to gain control over their own destiny.
Another suspect could be a rogue ninja from a hidden village that has a vendetta against Konoha. Naruto is a symbol of Konoha's strength, and by stealing his eyes, they could be trying to weaken the village both physically and symbolically. This ninja might have lost someone or something to Konoha and sees this as a way to get revenge.
In a 'Naruto has his eyes stolen' fanfic, the plot might revolve around a new, mysterious villain who targets Naruto specifically for his eyes. Maybe the villain believes Naruto's eyes hold some sort of special power or prophecy. Naruto, in his usual determined way, would not let this setback stop him. He could start training with Jiraiya again, this time focusing on his other senses to compensate for the loss of his eyes. His friends would be in a state of shock and anger, and they would split up to search for clues about the thief.
One possible motive could be power. Naruto's eyes might possess some unique power in this fanfic, like the ability to control a powerful jutsu or access some hidden knowledge. The thief could want to use this power for their own gain, perhaps to take over a village or defeat their enemies.
It could be a powerful rogue ninja who has a vendetta against Naruto specifically because of the gunblade. Maybe he was once part of a group that was tasked with protecting the gunblade, but it was lost under his watch, and he blames Naruto for having it now.
It could be a new, self - made villain. Maybe a rogue ninja who was once rejected by the Hidden Leaf Village. He blames Naruto for his misfortunes and decides to target his sister as revenge. This villain would have his own set of unique and dangerous jutsu, which Naruto would have to figure out how to counter in order to save his sister.
It could be a new character created specifically for the fanfic. Maybe a rogue ninja from a far - off land who has a vendetta against Naruto. This antagonist might be after Naruto's power or trying to stop him from achieving a certain goal.
It could be a new, powerful ninja who has a vendetta against Naruto. This antagonist might be jealous of Naruto's popularity and power, and wants to take over the Hidden Leaf Village.
It could be a new character. Maybe a powerful ninja from a far - off land who has heard rumors of Naruto's strength and is determined to draw it out and defeat him to prove his own superiority. This antagonist might be secretly spying on Naruto and trying to find ways to force him to show his true power.
It could be a powerful new villain who wants to get back at Naruto. Maybe someone from a rival village who thinks stealing his wife will weaken him.
It could be a rogue ninja from a forgotten clan who is jealous of Naruto's new - found power from his hidden bloodline. This antagonist might try to steal Naruto's bloodline ability for himself.