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.
Perhaps the plot involves Naruto getting the Mangekyou Sharingan as a gift from an unexpected source. It could be an old sage who sees Naruto's potential for using it for good. Naruto then uses the unique abilities of the Mangekyou Sharingan, like its powerful genjutsu or special doujutsu techniques, to fight new and stronger enemies, and at the same time, he tries to incorporate it into his own ninja way.
Well, it could be that Naruto gets the Mangekyou Sharingan in a parallel universe type of scenario. In this world, the power dynamics are different. Naruto, with his newfound power, has to deal with the internal struggle of using a power that was once exclusive to the Uchiha clan. He might struggle with the dark side of the Mangekyou Sharingan's power, but ultimately uses it to bring about peace in this alternate reality.
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.
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 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.
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.
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.
In this fanfiction, Naruto getting the eternal mangekyou sharingan might lead to him exploring his family's past more deeply. Since the sharingan has ties to the Uchiha clan, Naruto could discover some long - lost secrets about his own family's connection to the Uchiha. This could open up a whole new plotline where he uncovers hidden villages or techniques related to his family's history.
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.
Naruto's character would likely become more complex. He'd have to deal with new powers and the responsibilities that come with them. He might become more introspective as he tries to understand the nature of the Sharingan and how it fits into his ninja beliefs.
One possible triggering event could be the loss of a dear friend. Just like Sasuke's awakening of the Mangekyou Sharingan was related to the trauma of Itachi's actions. In a fanfiction, Naruto might witness the death of someone like Kakashi, who has been a mentor figure. This intense emotional pain and the sense of loss could be the catalyst for his Mangekyou Sharingan to awaken. It would add a new layer of depth to his character, as he would have to deal with this new power and the grief that came with its awakening.
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.