The plot could involve Mikoto's pregnancy being a symbol of hope for the Uchiha clan. With the unrest in the village, her unborn child could be seen as a new beginning. The story might show her interacting with other clan members who are both excited and protective. For instance, some of the older Uchiha might share their wisdom with her about raising an Uchiha child.
In the fanfiction, perhaps Mikoto is trapped in a genjutsu created by an enemy. Naruto, being very perceptive when it comes to such things, realizes something is wrong. He uses his own chakra to break through the genjutsu and then protects Mikoto from the caster of the genjutsu. This could lead to a bond forming between Naruto and Mikoto, with Naruto seeing her as a sort of mother figure since he lost his own parents early on.
One possible plot could be that Mikoto, perhaps having some special skills or knowledge, teams up with Naruto in a mission within the fanfiction world. They might face a powerful enemy together, and Mikoto uses her unique abilities to complement Naruto's. For example, if Mikoto has some sort of elemental control, she could combine it with Naruto's Rasengan to create a new and more powerful attack.
Perhaps in the fanfiction, Naruto is in a vulnerable state, like he's lost his powers temporarily. Mikoto, having a soft spot for him, takes it upon herself to be his guardian. She has to face not only physical threats from Naruto's enemies but also deal with the political situation in the ninja world that might put Naruto at risk. She uses her influence as an Uchiha to shield Naruto from all these dangers.
In this fanfiction, it could be that Mikoto's connection to the Nine - Tails is explored. Maybe she has some sort of special ability that allows her to sense the Nine - Tails' chakra within baby Naruto. She then tries to help Naruto control this power from a young age. She might introduce him to some spiritual practices or chakra - control methods that are unique to the Uchiha or something she has discovered on her own. This would completely change Naruto's journey as he grows up with better control over the Nine - Tails' power.
Well, it could be about Naruto being hypnotized by Mikoto into believing he has certain powers or a different identity. Maybe she hypnotizes him to help him overcome some fears or traumas.
The plot could revolve around Naruto learning about the Uchiha's history from Mikoto. Since she has a deep understanding of the clan. He might discover secrets that could help him in his journey to become Hokage. And Naruto could also be a positive influence on Sasuke, who might be less brooding with Naruto around. Mikoto would be like a mother figure to Naruto, guiding him in his studies and ninja training.
Well, one possible scenario could be that in this fanfiction, Naruto discovers Mikoto is pregnant and he takes on the role of a very protective friend. He might help her with daily tasks, like getting groceries or just being there for emotional support. Naruto's own experiences growing up without parents could make him extra determined to ensure Mikoto has a smooth pregnancy.
A great plot could be that Naruto discovers a hidden scroll that was once in the possession of both Kushina and Mikoto. This scroll contains a prophecy about a great threat to the ninja world that only the combined powers of the Uzumaki and Uchiha clans can defeat. Naruto then has to convince Kushina and Mikoto to work with him to decipher the scroll and prepare for the upcoming danger.
One possible plot could be that Mikoto, in her yandere state, becomes obsessed with Naruto. She might try to keep him away from his friends and training, believing that only she can protect him. For example, she could use her Sharingan abilities to spy on Naruto's interactions with others like Sasuke or Sakura, and then interfere when she feels Naruto is getting too close to them.
In this kind of fanfiction, one possible plot could be that Mikoto is in danger from an unknown enemy. Naruto, with his strong sense of justice and his powerful ninja skills, somehow discovers her plight. Maybe he stumbles upon a battle where Mikoto is outnumbered and on the verge of defeat. He then jumps into the fray, using his Rasengan or other signature moves to fend off the attackers and save her.