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.
The plot could involve Naruto having to deal with the side effects of having Nagato's eyes. Since the Rinnegan is a very powerful and complex dojutsu, it might have some negative impacts on Naruto's body or mind. He could struggle with visions or voices from the past users of the eyes. At the same time, he might use the eyes to uncover secrets about the origin of the ninja world and the true purpose of the tailed beasts.
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.
Well, in a fanfiction where Naruto has Sans eye, it could start with Naruto finding himself in a dimension where he's given this strange power. The Sans eye might give him a new perspective on the concept of chakra, perhaps seeing it in a different form or being able to manipulate it in ways he couldn't before. He could use this new power to better understand his enemies and their motives, and it could also create some interesting interactions with his friends who would be both amazed and a bit wary of this new power.
In a fanfic where Naruto takes Nagato's eyes, he might gain new and powerful abilities. For example, he could potentially access the Rinnegan's powers more directly. This could make him even stronger in combat, perhaps allowing him to use abilities like the Six Paths Techniques with greater ease. It could also change his relationships with other characters. Some might be in awe of his new power, while others could be afraid or jealous.
Well, one possibility is that Naruto gains new powers with the Rinnegan. He might use it to finally bring true peace to the ninja world. Maybe he could combine the power of the Rinnegan with his existing Sage Mode and Nine - Tails chakra, becoming an even more formidable force against any threats.
One possible plot could be that Naruto's kid discovers their own unique ninja abilities. Maybe they struggle at first to live up to Naruto's legacy but then find their own path. For example, they might be more interested in healing jutsu rather than combat like Naruto was.
One possible plot could be that Naruto discovers the nanites in his body accidentally. They might enhance his abilities like his chakra control or give him new powers. For example, the nanites could help him to better manipulate his shadow clones, making them more efficient in battle.
One possible plot could be that Naruto discovers he has Shisui's eyes through some sort of ancient Uchiha ritual or curse that was unknowingly transferred to him. Mikoto could be the one who reveals the truth about his newfound powers. Then Naruto has to learn to control the Sharingan while also dealing with the Uchiha clan's secrets that Mikoto is aware of.
Maybe his special eyes allow him to see into the past. He could witness the great ninja wars as if he were there. This would help him understand the history of the ninja world better and gain wisdom from the past. He might see how his father, Minato, fought in the wars and learn new jutsu from those memories.
Well, one possibility could be that Naruto discovers his relation to Nagato early on. This might lead to a whole different dynamic in the story. Maybe Nagato would be more hesitant to fight Naruto, and Naruto could try to understand Nagato's pain from a more personal perspective, instead of just seeing him as an enemy. It could also mean that Naruto has access to some of Nagato's knowledge or abilities in a unique way.