Well, perhaps a plot twist could be that the Fem Shinigami was actually sealed away for a reason, and Naruto's existence starts to unseal her power bit by bit. As a result, he has to deal with the consequences of this power emerging within him. He might start to have visions of the Shinigami realm and be haunted by the souls that his mother was supposed to deal with. This could make him question his own identity and purpose.
A really interesting plot twist could be that Naruto's status as the son of the Fem Shinigami is a closely guarded secret. Only a few people like the Third Hokage know about it. When Orochimaru discovers this secret during the Chunin Exams, he tries to capture Naruto to use his Shinigami - related powers for his own immortality experiments. Naruto then has to not only fight Orochimaru but also protect the secret of his heritage.
One possible plot twist could be that Naruto has the ability to control the souls of the dead, inherited from his mother, the Fem Shinigami. This could lead to him being able to communicate with past Hokages in a more direct way than just through their chakra imprints. Another plot twist might be that Naruto has to face an enemy who is also related to the Shinigami realm and his connection to it is the key to victory.
Perhaps a plot twist could be that the village initially rejects Naruto due to his relation to Fem Madara. They fear he might turn out like his mother and bring destruction. This would force Naruto to prove himself in a different way than in the original series. He might have to find allies outside the village and then come back to redeem himself in the eyes of the villagers.
Well, it could be about Naruto having some special powers or abilities related to being the son of a Shinigami. Maybe he can communicate with the dead more easily or has some sort of death - related jutsu.
One possible plot twist could be that Fem Naruto discovers she has a unique hidden power that is related to the Yamanaka clan's abilities. Maybe she can combine her Uzumaki chakra with their mind - related jutsu in an unexpected way.
One possible plot twist could be Naruto having to deal with the expectations of the Greek pantheon. Since Athena is known for her wisdom, Naruto might struggle to live up to that intellectual standard while still maintaining his ninja way. For example, in battles, he might be expected to use more strategic thinking rather than just brute force.
It could be about Naruto having a connection to the Shinigami. Maybe it explores a story where Naruto is the son of the Shinigami in an alternate universe. It might involve Naruto having special powers or a different destiny related to the Shinigami's realm.
I'm not entirely sure as it depends on the specific fanfiction. But generally, it might involve Naruto having some sort of divine or shinigami - related origin, which could lead to him having special powers or a different path in his ninja journey.
The plot might involve Naruto being sent to the Shinigami realm for some reason. There, he has to adapt to the rules and powers of the Shinigami. He could make allies among the Shinigami and bring back some of their knowledge and powers to his own world, causing a stir among the ninja clans. He might also face challenges from Shinigami who don't trust him at first because he's an outsider.
One possible plot twist could be that their union causes a rift in the ninja world. Some might oppose it due to Itachi's past actions. Another could be that Fem Naruto discovers a hidden power within herself as a result of their marriage bond. It could also be that an old enemy resurfaces to target them because of their combined strength and the new hope their union represents for the future of the ninja villages.
It could be that Fem Sasuke is under some sort of mind - control when she kidnaps Naruto. A powerful enemy, like Orochimaru or a new villain, might have used a jutsu to make her do this. As the story progresses, Naruto would then have to find a way to break the mind - control on Fem Sasuke while also dealing with the situation of being kidnapped.
One possible plot twist could be that their relationship is initially opposed by the village elders. They might see it as unconventional or worry about how it could affect Naruto's role as a potential Hokage. Another twist could be that an old enemy resurfaces and targets Kakashi to get to Naruto, seeing their marriage as a weakness to exploit.