One interesting concept could be new and unique jutsu. For example, the author might create a jutsu that combines the powers of the eternal mangekyo in a way that has never been seen in the original Naruto series. Another concept could be different character relationships. Maybe in the fanfiction, characters who were enemies in the original become allies, all because of the power of the eternal mangekyo.
Naruto would likely become more introspective. The Mangekyo Sharingan often comes with a lot of emotional baggage in the Naruto universe. So, Naruto might start to question his own identity more, especially since this power is from a clan he has no blood relation to. He could also become more cautious as he learns about the potential dangers of misusing the Mangekyo Sharingan.
It could be an original character. Maybe a young ninja from a small, forgotten clan who discovers they have the Mangekyo Sharingan. This character would have to learn about their power, its limits, and how to use it in a world full of powerful shinobi.
Naruto is usually a main focus, as the title implies it has to do with his connection to the eternal mangekyo. Sasuke is also often a key character. Their relationship and how it changes due to Naruto having the eternal mangekyo powers can be a major part of the story.
One common theme is power struggle. When a Harry Potter character gets the Eternal Mangekyo Sharingan, they have to deal with the new power and how it affects their relationships. Another theme is identity. They might question who they are now that they have this new ability from a different universe. For example, a Gryffindor might struggle with the more 'ninja - like' aspects of the Sharingan that seem at odds with the Gryffindor values.
Another concept is the character development. The presence of the Eternal Mangekyo Sharingan often brings a deeper level of conflict and growth for the characters. They might have to struggle with the power it bestows, such as the risk of going blind or the moral implications of using its more sinister abilities.
Another plot could revolve around a character who has the Mangekyo Sharingan but is trying to hide it from both their allies and enemies. They fear the power it holds and the attention it might draw. As the story progresses, they are forced to use it in a crucial battle, and their friends then have to deal with the revelation and the potential danger it brings to the group.
One possible plotline could be Naruto unlocking the Mangekyo Sharingan through some strange and unforeseen means, perhaps a powerful jutsu backfires and gives him this new power. Then he has to struggle with controlling it while his friends are both amazed and a bit worried about this new development in him.
For Kakashi, if he were to gain an enhanced Mangekyo Sharingan in this crossover, his relationship with his students would shift. He would be even more of a figure of power and mystery to them. His interactions with Naruto might become more about teaching him how to counter the Sharingan's powers, as Naruto would be facing more powerful Sharingan - users. And his relationship with Sasuke could become more strained, as Sasuke might see Kakashi's new power as something he wants to surpass even more urgently.
One interesting plot idea could be a character from the Naruto world obtaining the Mangekyo Sharingan through some strange and unforeseen event. For example, Naruto himself could be exposed to a powerful Uchiha - related jutsu that accidentally gives him the Mangekyo Sharingan. This would completely change his power dynamic and how he approaches battles. He could then have to learn how to control this new power while still maintaining his own ninja way.