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.
Well, the fanfic could start with Naruto being in a strange part of the forest and stumbling upon Shisui who is in hiding. Shisui, initially cautious, soon warms up to Naruto when he sees Naruto's unwavering belief in friendship. They then start sharing their stories. Shisui tells Naruto about the Uchiha clan's past and his own struggles. Naruto, in turn, tells Shisui about his dreams of becoming Hokage. This encounter could lead to Shisui using his influence to help Naruto gain more support within the village and also give Naruto some insights into the Sharingan and how to counter it if he ever faces an Uchiha opponent.
Another possible antagonist could be a rogue Uchiha. One who didn't agree with Shisui's views on peace. This rogue Uchiha could see Naruto as an outsider interfering with Uchiha matters and Shisui as a traitor for teaming up with Naruto. So they set out to disrupt their partnership and cause chaos in the village.
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.
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.
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.
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 plot could be that Naruto goes on a special training journey with Jiraiya again, but this time they encounter a new and powerful enemy that has a connection to Jiraiya's past. Naruto has to learn a new jutsu from Jiraiya to defeat this foe.
One possible plot could be that Naruto is somehow sent back in time and meets his mother Kushina. He gets to know her as a person, not just as the mother he never really knew. They could train together, and Kushina could share some of her unique Uzumaki clan techniques with Naruto.
Well, the plot could involve Naruto and Meliodas teaming up to fight a common enemy. Maybe an evil force that threatens both their worlds. Naruto's ninja skills and Meliodas' demon powers would make for an epic combination in battles.
One possible plot could be that Naruto, in his journey, stumbles upon a succubus. The succubus might initially be attracted to Naruto's strong chakra. She could try to use her powers on him, but Naruto, being Naruto, resists with his determination. Maybe he tries to understand her instead of immediately fighting, leading to an unlikely friendship.
One possible plot could be that Naruto gets lost in a strange land where Konan is the protector. They meet, and at first, Konan is wary of Naruto as he's from Konoha. However, as they interact, they discover they both have a strong desire for peace in the ninja world. So, they work together to bring about a truce between their respective groups.