Perhaps the fanfic could focus on a training arc. A young ninja, who is a big fan of Shisui, discovers a way to inherit or mimic the abilities of Shisui's eyes through some special training method. This training would be filled with difficulties and self - discovery. As they progress, they start to understand the true burden that comes with such power. They might also attract the attention of some of the village's elders or enemies, which would lead to various conflicts and adventures.
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.
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.
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.
One possible plot could be that Naruto accidentally travels back in time and meets Shisui. Shisui, seeing Naruto's potential, decides to train him in some of his unique jutsu. This would give Naruto an edge in his future battles and also a new perspective on the Uchiha clan.
One possible plot could be that Naruto grows up with a different understanding of the Uchiha clan because of his connection to Shisui. He might be more involved in Uchiha affairs from an early age. For instance, he could try to prevent the Uchiha massacre, using his and Shisui's combined influence.
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.
Well, he might gain the power of Shisui's Sharingan abilities. Naruto could potentially use Shisui's powerful genjutsu skills. It would make him even more formidable in battles against tough opponents like the Akatsuki members.
One plot idea could be a story where a young ninja discovers they have received Shisui's eyes through some mysterious means. They then have to learn to control the unique powers of the eyes, like the powerful genjutsu abilities. This could lead to them being hunted by those who want to use the eyes for evil purposes.
The mystery surrounding the eyes is also appealing. In the Naruto universe, there are always secrets. With Shisui's eyes, there could be secrets about their origin or even some hidden powers that were not fully explored in the original series. A fanfic could dig into these mysteries. Also, the psychological impact on the character who has the eyes is important. These eyes are a great power, and with great power comes great responsibility. How does the character deal with the pressure? Do they become paranoid or do they rise to the occasion? This can be a great area to explore in the fanfic.
Perhaps the plot twist is that Shisui faked his death not just to protect the village in the general sense, but specifically to keep Naruto safe. He knew of Naruto's importance as the Jinchuriki of the Nine - Tails and his relation to Naruto as a brother. So, he went into hiding and has been secretly guiding Naruto from the shadows all along. This would add a whole new layer to Naruto's journey and the events that have unfolded in the series so far.