The plot of the fanfic where Naruto gets the Mangekyou Sharingan could involve him having to hide it from his enemies. If word got out, he could become a prime target. His training with the new power would be a major part of the story. He might have to seek out Uchiha survivors or scrolls to learn about the Sharingan's full potential. Also, this new power could potentially create a rift between him and his teacher, Kakashi, who also has a Sharingan. Kakashi might be both proud and worried about Naruto's new power.
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.
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.
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.
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 the fanfic, Naruto having the Eternal Mangekyou Sharingan could lead to a change in his relationships. His friends might be both in awe and a bit worried about this new power he has. Sasuke, being an Uchiha, could have a complex reaction. Maybe they would train together to better understand and control this power. Naruto could also use it to try and bridge the gap between the Uchiha and the rest of the village even more, as he now has a part of the Uchiha heritage in a very powerful way.
One possible plot could be that Naruto gains the Eternal Mangekyou Sharingan through some sort of unexpected and mysterious event. Maybe it's a result of a powerful jutsu gone wrong that fuses his own chakra system with that of a Sharingan - user. This new power could initially be difficult for Naruto to control, leading to him having to isolate himself to figure it out. As he masters it, he could use it in unique ways, like combining the Sharingan's abilities with his own Rasengan techniques, creating entirely new and powerful attacks.
The plot could involve some sort of time - travel or alternate dimension scenario. Naruto could be sent to a parallel world where the Uchiha clan was never massacred. There, he befriends the Uchiha and learns their ways. Eventually, he earns the right to receive the Eternal Mangekyou Sharingan through his deeds and his strong bond with the clan. With this new power, he has to find a way to return to his own world and use it to protect his friends and village from a new, greater threat.
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.
For his relationship with Kakashi, it could be complex. Kakashi, having his own experiences with the Sharingan, would be in a unique position to guide Naruto. But at the same time, he might be worried that Naruto's new power could attract unwanted attention. Naruto's bond with the villagers could also be affected. Some might see him as more of an Uchiha than a Uzumaki now, and there could be those who fear his power. His relationship with Jiraiya, if he were still alive in the fanfic, would also change. Jiraiya would need to teach Naruto how to use this power for good and not let it corrupt him.