One idea could be exploring a different origin for the Mangekyou Sharingan. For example, what if it was related to an ancient Uchiha pact with a hidden spirit? Another could be a story where a non - Uchiha character somehow gains the ability to use the Mangekyou Sharingan and has to deal with the consequences. Or perhaps a fanfiction where the Mangekyou Sharingan has additional powers that are not shown in the original Naruto series, like the ability to time - travel.
Another idea is a crossover with a superhero universe. Imagine a character like Sasuke with his Mangekyou Sharingan powers suddenly in the Marvel or DC universe. He could team up with heroes like Spider - Man or Batman. His Sharingan's ability to copy moves could be really interesting when facing off against super - villains.
One idea could be a story where the protagonist discovers a new and unique power within the Mangekyou Sharingan that has been lost for generations. This power could give them an edge in battles against powerful foes like the Akatsuki. Another plot could revolve around a character who has to overcome the dark side effects of using the Mangekyou Sharingan, such as losing their sight at a faster rate. They could search for a way to counter this while still using the power to protect their village.
A possible plot is that Naruto gets the Mangekyou Sharingan in a fight against a powerful enemy. With this new ability, he is able to see the enemy's weaknesses more clearly. He could use the unique abilities of the Mangekyou Sharingan, like Tsukuyomi or Amaterasu, in his own unique way, since he is not an Uchiha. For example, he might combine it with his Rasengan. This would lead to new and exciting battles and also a journey of self - discovery as he tries to understand this alien power within him.
A possible plot could be that Dark Naruto's Eternal Mangekyou Sharingan has a special power that can merge the minds of people. He uses this to merge with the good Naruto inside him. Through this merge, he battles his inner demons and slowly transforms back to his normal self while also gaining the combined strength of both his dark and light sides.
One idea could be exploring how Itachi uses his Eternal Mangekyou Sharingan to change the past. Maybe he goes back in time to prevent the Uchiha massacre and has to deal with the consequences of altering such a major event in the ninja world.
One idea could be a story where Naruto somehow acquires the Mangekyou Sharingan and Rinnegan. He then has to learn to control these new powers while facing an ancient evil that only he can defeat with the combined might of these dojutsu. Maybe he teams up with Sasuke, who also has his own power upgrades, and they have to figure out how to merge their abilities to save the ninja world.
One creative plot twist could be a character who was thought to be a normal ninja suddenly reveals they have a Mangekyou Sharingan with a unique power that changes the whole power dynamic in the story. For example, a side character who has been helping the main character all along, but then uses their Mangekyou Sharingan to stop an impending doom that no one else could. Another could be that the Mangekyou Sharingan has the ability to swap the powers of other ninjas, creating chaos and new alliances.
One popular plot idea could be a character with Mangekyou Sharingan traveling back in time to prevent a major tragedy in the Naruto universe. For example, stopping the Uchiha massacre. This would create a whole new set of events and relationships. Another idea might be a time - traveling ninja using the power of the Mangekyou Sharingan to gain knowledge from the past and use it to change the future of their clan. They could learn ancient jutsu or secrets that were lost over time.
In many Naruto fanfictions, Itachi is often depicted as an extremely powerful Mangekyou Sharingan user. His original abilities in the canon, like Amaterasu, are further enhanced in fan works. Sasuke is also a common focus. His Mangekyou Sharingan's powers can vary greatly from one fanfiction to another, sometimes with new and unique jutsu created by the authors. Another character could be Madara. Fanfiction writers love to explore the full potential of his Mangekyou Sharingan, often giving him abilities that were only hinted at in the original series.
In such a fanfiction, one possible plot could be that Naruto acquires the Mangekyou Sharingan through some kind of magical or experimental accident. Maybe a powerful enemy uses a jutsu that backfires and transfers the Sharingan to Naruto. Then Naruto has to learn to control its power while also facing the prejudice from those who fear the Sharingan's abilities.