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.
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.
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.
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.
One possible plot could be that in the fanfiction, a villain uses hypnosis on Mikoto Uchiha to make her turn against the Hidden Leaf Village. Naruto, being the hero, has to find a way to break the hypnosis. Maybe he discovers a special jutsu that can counter the hypnosis magic. He then has to face off against the villain while also trying to reach Mikoto and bring her back to her senses.
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.
Well, one possibility could be that Naruto uses his ninja skills to protect Mikoto and Hitomi from some common enemy in the Naruto universe, like rogue ninjas. Maybe they are on a mission together and Naruto's strength and quick thinking come in handy to keep them safe.
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.
Well, in this kind of fanfiction, Naruto might grow up with a different kind of family environment. He could be influenced by the Uchiha clan's traditions and values. Maybe he would learn some Uchiha - specific jutsu earlier. And he would probably have a closer relationship with Sasuke from the start as they would be like brothers in a sense.