One possible plot twist could be that Naruto's new Mangekyou Sharingan gives him the ability to access a new form of Sage Mode. Since the Sharingan has unique powers and Sage Mode is Naruto's own power, their combination might create something unexpected. For example, he could use the Sharingan to better target his Sage chakra, making his attacks more precise and powerful.
The Mangekyou Sharingan could also create an internal conflict within Naruto. He has always been a firm believer in his own power and the power of friendship. But with the Sharingan, he might start to rely on its power too much. This could lead to a struggle within himself as he tries to figure out how to balance his old values with the new abilities and temptations that come with the Mangekyou Sharingan.
Maybe the implanted Mangekyou Sharingan causes Naruto to have visions of the Uchiha clan's past. This could lead to him understanding the Uchiha's pain and hatred on a deeper level. As a result, he might try to bridge the gap between the Uchiha and the rest of the village in a different way than before, using his new insights to bring about peace.
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.
A plot twist could be that Naruto receives the Mangekyou Sharingan from Sasuke in a self - sacrificing moment. Sasuke, realizing the true potential of Naruto's power combined with the Sharingan, decides to transfer his Mangekyou Sharingan to Naruto. This would create a whole new dynamic in their relationship. Naruto would then have to master the abilities of the Sharingan quickly to face an impending and powerful threat to the Hidden Leaf Village.
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 possible plot twist could be that Naruto gains the Mangekyou Sharingan in a moment of extreme emotional turmoil, like seeing Sasuke in a life - threatening situation. This new power might make him an outcast in Konoha at first, as the Sharingan is a symbol of the Uchiha. Another twist could be that the Mangekyou Sharingan has some unforeseen side effects on Naruto's chakra system, making it difficult for him to control his normal jutsu. It could also lead to a power struggle within the village as some might fear Naruto's new - found power.
The character with the Mangekyou Sharingan might lose their eyesight due to overuse in the new and unfamiliar world of the crossover, but then gain a new form of power that is related to the crossover world. Maybe they lose their Sharingan sight but gain the ability to see magic auras or something similar. This would be a huge twist for both the character and the readers.
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.
With Sasuke, their relationship would become more complex. Sasuke might be both jealous and intrigued by Naruto having the Mangekyou Sharingan. Jealous because it was always an Uchiha thing, and intrigued because he wonders how Naruto will use it. This could lead to more intense rivalries and also more opportunities for them to understand each other better.
Perhaps in the fanfiction, Naruto discovers a hidden connection between his Uzumaki heritage and the Sharingan. This newfound knowledge, combined with a great battle against a powerful villain, causes the Mangekyou Sharingan to awaken. It could also involve some sort of ancient prophecy or power that was long forgotten, and Naruto is the key to unlocking it which leads to the awakening of his Mangekyou Sharingan.
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.
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.