Maybe Naruto's red eyes are a result of a genetic experiment that was secretly carried out in the village long ago. This revelation could cause a stir in the Hidden Leaf. Naruto would then be at the center of a political and moral debate. Some would see him as a threat, while others, like his true friends, would stand by him and help him uncover the truth about his origin and the significance of his red eyes.
The plot could involve Naruto's red eyes being the key to an ancient prophecy. People from other villages might try to capture him to use his eyes for their own gain. Naruto, along with his friends, would have to go on the run and protect himself while also trying to figure out the true meaning behind his red eyes.
The plot might involve Naruto getting Shisui's eyes in a strange accident. With these eyes, he discovers a hidden conspiracy within the Hidden Leaf Village. There are some rogue ninjas who are planning to use a powerful jutsu that can only be countered with the unique abilities of Shisui's eyes. Naruto, with his new - found powers, has to team up with his friends like Sasuke and Sakura to expose the conspiracy and save the village. Along the way, he struggles with controlling the Sharingan's powers and the emotions that come with it.
A great plot could involve a mysterious figure who implants the Byakugan into Naruto for an unknown purpose. Naruto starts to see the world in a different way with his new eyes. He can now sense danger more easily and even predict his opponents' moves better. The story could then revolve around Naruto trying to find out who did this to him and why. Along the way, he teams up with some Hyuga members who teach him the secrets of the Byakugan, and together they face a common enemy that threatens the entire ninja world.
One possible plot development could be that Naruto becomes a target. Since Shisui's eyes are so powerful, other villages or rogue ninja might want to take them from Naruto. This would lead to a lot of battles and Naruto having to constantly defend himself. Another development could be that Naruto tries to master the abilities of the Sharingan quickly. He might seek out people who know about the Sharingan, like Kakashi or Sasuke, to train with.
One plot implication could be that Naruto is initially distrusted by some in the village. They might see the Sharingan as a symbol of danger or the Uchiha's past misdeeds. This could create internal conflict within the village. Also, Naruto might be hunted by enemies who fear the power of the Sharingan in his hands.
One great fanfiction is 'The Fox - Eyed Naruto' on FanFiction.net. It really delves into how Naruto's fox - eyed appearance changes the way people perceive him in the village. The author does an amazing job of integrating this new physical trait into the existing Naruto universe storyline.
One possible plot could be that Naruto discovers Crescent Rose in a strange new world he accidentally gets transported to. He has to learn how to use it while also finding his way back home. Along the way, he might face enemies that are only vulnerable to Crescent Rose's attacks.
The plot could involve Naruto finding Sode no Shirayuki during a mission in a hidden land. He starts to have strange dreams related to the sword's past. As he delves deeper into understanding the sword, he discovers that it has a connection to an ancient clan. This connection leads him on a journey to uncover secrets that could change the shinobi world.
One possibility is that it gives him a more mysterious and alluring look. In fanfiction, authors often use physical changes to symbolize a character's inner transformation or special powers. Black hair and red eyes might signify a new, more powerful Naruto, perhaps with a connection to some ancient or dark power source.
In a Naruto fanfiction with red eyes, he might gain this trait as a result of a new power-up. For example, he could encounter a powerful sage or a mysterious entity that bestows him with this red - eyed form. His abilities would likely change as well. He could have enhanced perception, like being able to see chakra more clearly or even predict his opponents' moves better. His friends might be initially shocked but would soon accept this new Naruto as he uses his powers for the good of the village.
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.