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 can drive the plot forward in many ways. His luck often leads to new opportunities for growth and power - ups. For example, if he finds a special item by luck, it might unlock a new ability for him, which then changes the direction of the story as he has to learn to control this new power.
It can create new challenges. For example, if Naruto can sense everything, the villains might have to come up with more elaborate ways to hide their plans or their presence, which drives the plot forward as they develop new strategies.
It can be a plot - saving device. For example, if a major character is severely injured in a battle, Naruto's healing jutsu can bring them back from the brink of death, changing the course of the story. Instead of a character dying and leading to a dark and tragic turn, they survive and contribute to future events.
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.