Well, in fanfiction where Naruto has a Sharingan, a great plot twist could be that the Sharingan was actually a cursed version. It gives him great power but also slowly drains his life force. This would create a race against time for Naruto to find a cure while still using the power to protect his village. Another plot twist could be that the Sharingan unlocks memories of a past life where Naruto was an Uchiha. This would make him question his identity and his role in the ninja world. And if his Sharingan had the ability to control the Nine - Tails directly, without the need for complex seals, that would completely rewrite the rules of his power.
One interesting plot twist could be that Naruto's Sharingan was a result of some ancient prophecy or hidden experiment. This would make him an even greater target for villains. Another could be that his Sharingan has a unique ability different from other Uchiha's, like being able to see the true intentions of people. This would change how he interacts with everyone in the ninja world.
Imagine a plot twist where the Sharingan and Rinnegan are not unique to the ninja world. In a fanfiction, it could be revealed that an alien race has similar powers. A character from Naruto's world travels to this alien planet and discovers that their understanding of these powers is completely different. They must then adapt to this new knowledge and use it to save both worlds from a common enemy that is drawn to the power of the Sharingan and Rinnegan.
In some fanfictions, the Sharingan is used to explore the history of the Uchiha clan from a different perspective. For instance, a story could focus on a young Uchiha who is born with a defect in their Sharingan. Through their journey, they discover secrets about the origin of the Sharingan that were long forgotten by the clan, and this knowledge could potentially change the future of the Uchiha and the entire ninja world.
One idea could be that Naruto discovers he has these powers due to some ancient curse or blessing. He then has to hide it from his friends at first because he doesn't understand it. As he starts to master it, he uses it to protect the village in unexpected ways, like using Mokuton to quickly rebuild damaged areas after an attack while using Sharingan to detect any remaining threats.
An interesting plot could be that Naruto, with his new eyes, discovers a hidden conspiracy in the ninja world that was related to the origin of the Rinnegan and Sharingan. He has to use both his powers to uncover the truth and stop those behind it. For example, he might find out that there is a group that wants to control all the powerful ocular jutsu in the world. With the Sharingan, he can detect their lies and with the Rinnegan, he can take on their powerful minions. Also, he could use the powers to communicate with ancient ninja spirits and gain their wisdom to solve current problems.
One plot idea could be a character who is an experiment and has only one Sharingan eye implanted. They struggle to control its power and are hunted by those who want to use their unique situation. For example, they might have to constantly fight off rogue ninjas who think they can steal the eye's power.
One plot idea could be a character who was born with only one Sharingan eye and has to struggle to master its powers in a world where most Uchiha have two. They might face discrimination from their clan for being different. Another idea is that a character loses one of their eyes in a battle and then has to adapt to having just one Sharingan, with different abilities emerging as a result of this change. For example, the single Sharingan could have enhanced perception abilities to make up for the lack of a second eye.
One possible plot twist could be that Naruto's Sharingan has unique abilities not seen in the regular Uchiha Sharingan. Maybe it can combine with his Sage Mode in unexpected ways, like seeing chakra flows more clearly even in Sage Mode, enhancing his combat skills.
One possible plot twist could be that Naruto struggles to control the Sharingan at first. Since he's not from the Uchiha clan, the Sharingan's powers might act differently in him. For example, instead of the normal abilities like predicting movements, it might give him visions related to the Uchiha's past traumas. This could lead to Naruto having to deal with not only the power of the Sharingan but also the emotional baggage that comes with it.
One possibility could be through a forbidden jutsu experiment gone wrong. Maybe some rogue ninja was trying to create a super - powered being and Naruto ended up being the subject. The Sharingan was transplanted into him, but only one eye was successful.
In some fanfictions, he might obtain it through a powerful jutsu gone wrong that somehow fuses Uchiha DNA with his own. Maybe during a battle where he's exposed to some strange chakra energy related to the Sharingan.