Brainwashed Mikoto can have a huge impact on the plot. She could be used to start conflicts. For example, if she attacks other characters without reason due to the brainwashing, it would lead to battles and new rivalries.
In a Naruto fanfic where Mikoto is brainwashed, she could be made to do things against her normal nature. For example, she might be forced to fight against her friends or family. Maybe she'll be used as a tool by the villains in the fanfic's plot to gain some advantage over the other characters. It really depends on the creativity of the fanfic writer.
It can create new conflicts. For instance, other villages might see the superhuman - bodied character as a threat and try to eliminate them.
Well, it could be that Mikoto is trapped in a dangerous situation like a collapsing building or a genjutsu. Naruto, with his strong will and powerful chakra, breaks the genjutsu or rescues her from the rubble. He might sense her distress using his Sage Mode or his connection to the Nine - Tails' chakra and rush to her aid.
Mentally, Naruto would grow in a different way. He wouldn't have to rely solely on his pranks to get attention. Mikoto could guide him in a more positive way, helping him understand his own strength and the importance of his Uzumaki heritage. And with the Uchiha name attached to him, at least in the context of the adoption, he might face different challenges and opportunities within the ninja world.
It could mean that Mikoto really loves reading or writing Naruto fanfiction. Maybe she spends a lot of her free time immersed in the world of Naruto created by fans, exploring different storylines and characters that are not in the original manga or anime.
One possible plot could be that Mikoto somehow survived and she takes Naruto under her wing. She trains him secretly, using her Uchiha knowledge to make him stronger. This could lead to Naruto having a unique set of skills that no one else has.
The plot could revolve around a mystery in the village that only Kushina, Mikoto and Naruto can solve. Maybe there are strange disappearances that are related to an ancient power that was once sealed by the Uzumaki clan and has some connection to the Uchiha. Kushina uses her knowledge of the Uzumaki history, Mikoto her understanding of the Uchiha lore, and Naruto his unique perspective as the Jinchuriki of the Nine - Tails. They have to overcome their differences and work together to save the village from this hidden threat. Along the way, they develop a deeper bond as they face various challenges.
A possible plot is that Mikoto stumbles upon baby Naruto in the forest. She takes him back to the Uchiha compound. There, she raises him as one of their own, much to the confusion of some Uchiha members. As Naruto grows, he starts to show unique abilities that are a combination of his Uzumaki heritage and the influence of the Uchiha environment.
Well, it could be about Mikoto seeing Naruto's lonely situation and deciding to take him in. Maybe she'd teach him some Uchiha techniques and help him grow stronger. She could also introduce him to Sasuke as a brother figure, changing the whole dynamic between Naruto and Sasuke in the Naruto world.
Well, perhaps in this fanfic, Naruto being raised by Mikoto means he has a more stable and loving upbringing. He could be friends with Sasuke from a very young age, and they might grow up like brothers. Naruto would also be exposed to the Uchiha's rich history and culture, which could shape his understanding of the ninja world and his own place in it. He might even get to know some secrets of the Uchiha clan that no one else outside the clan knows.