Well, Naruto would likely gain a different perspective on the Uchiha. Mikoto could share stories about Itachi and Sasuke when they were younger. This would make Naruto understand Sasuke on a deeper level. For example, he might realize why Sasuke is so driven by revenge and be better equipped to handle their relationship.
One possible storyline could be that Naruto learns unique skills from Mikoto. Maybe she teaches him some of the Uchiha clan's secret techniques, like fire - based jutsu, which would be really interesting as Naruto is mainly associated with wind - style. This could also lead to Naruto having a closer connection to the Uchiha, which would change his relationships within the village.
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.
Perhaps Mikoto sees Naruto's potential not just as a shinobi, but as a person who can bring about change. She could train him in areas like stealth and intelligence - gathering, skills that are crucial for a ninja. Naruto, with his determination, would quickly pick up on these skills and use them to protect the village in ways he hadn't before.
Being Mikoto's apprentice might also give Naruto a different perspective on life. Mikoto could share her wisdom and experiences with him, which would help him grow not just as a ninja but also as a person. Her teachings could influence his leadership style if he becomes Hokage in the future, making him more empathetic and well - rounded.
Naruto could learn the art of poison from Sasori. Since Sasori was known for his use of poison in his puppets, Naruto might find a way to use it defensively, like coating his kunai with a non - lethal poison that just immobilizes enemies.
One possible scenario is that Naruto would gain a lot more knowledge about the village's history and politics. The Sandaime, being an experienced Hokage, could teach Naruto about the different clans in the village, their relationships, and how to manage them. Naruto might also learn more advanced jutsu more quickly, as the Sandaime could give him personal training. This could make Naruto a much stronger ninja at a younger age and perhaps change the course of some of the earlier story arcs.
Well, they could become rivals. Since Naruto is always striving to be the best and Mikoto, being from the Uchiha clan, would also be highly competitive. They might compete in various ninja tasks and exams, constantly pushing each other to improve.
The apprentice could be a new genin who shows great potential in the field of intelligence gathering. Maybe someone with a sharp mind and an ability to stay calm under pressure, like Shikamaru. He has the intelligence and strategic thinking that would make him a good candidate for Ibiki's apprentice.
In this fanfiction, perhaps Mikoto could teach Naruto some unique Uchiha techniques. Since she's from the Uchiha clan, she might have insights into fire - style jutsu that could help Naruto diversify his skills.
The apprentice could learn unique jutsu from Orochimaru. Since Orochimaru is known for his forbidden jutsu, the apprentice might gain an edge in combat but also face the danger of being corrupted by the power. They could then use these skills in battles against common enemies. And, in the process, they might try to redeem Orochimaru in some way, like showing him that there is a better path than his thirst for power.