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 also be for a ritual. In some fanfic settings, there are dark rituals that require special body parts. Naruto's eyes, being unique, might be a key ingredient for a ritual that the thief is trying to perform. This could be to summon a powerful demon or gain immortality.
Another motive could be revenge. Maybe someone Naruto has defeated in the past, or someone related to them, wants to take something precious from him as payback. By stealing his eyes, they are not only causing him physical harm but also robbing him of his potential power.
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.
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.
One possible storyline could be that Naruto's new 'four eyes' are a result of some strange jutsu gone wrong. Maybe he was trying to enhance his perception skills and ended up with an extra pair of eyes. These eyes could give him unique abilities, like seeing different types of chakra more clearly or even predicting an opponent's moves better. He might struggle at first to control this new change and it could be a source of both humor and growth in the story.
One possibility is that Naruto gains new powers. With Nagato's eyes, he might be able to use the Rinnegan abilities in unique ways. For example, he could master the Six Paths techniques more quickly. Another aspect could be the change in his relationships. His friends might be both in awe and a bit wary of his new power. And he would have to learn to control these new abilities to avoid being consumed by the power of the Nagato eyes.
Well, it could start with Sasuke being in a really dangerous situation where he's about to lose his eyes but Naruto intervenes. In the process, some sort of jutsu backfires and Naruto ends up with Sasuke's eyes. This would cause a huge shift in Naruto's relationships. His friends would be both worried and curious. And Naruto would be on a journey to master these new eyes while also trying to find a way to give them back to Sasuke if possible.
One possible plot could be that Naruto gains Shisui's eyes through some mysterious ninja art. With these eyes, he could have enhanced perception abilities, like being able to see through genjutsu more easily. This would change his fighting style and make him even more formidable against opponents. He might also use the unique powers of Shisui's eyes to uncover hidden secrets in the ninja world, leading to new adventures and alliances.
One possible motive could be a dark or alternate universe take. Maybe in this fanfic's world, there is some sort of dark magic or mind control that forces Naruto to do it against his will.
One possible motive could be jealousy. Maybe the sister is jealous of Naruto's popularity, his strength, or the attention he gets from others in the village.
One possible motive could be if his brother was somehow a threat to the village. Naruto is very loyal to Konoha, so if his brother was planning to destroy it or harm its people, Naruto might feel compelled to stop him at all costs.