Well, the plot could involve Naruto being trained in a very different way. Since he's the son of Minato and Mikoto, he might be taught a blend of the Namikaze and Uchiha techniques. For example, he could learn to combine Minato's Flying Thunder God Technique with some basic Uchiha fire - style jutsu. And there could be a story arc about how he unites the two clans that his parents come from, which have had some historical tensions. He would have to use his unique heritage to bring peace between them.
Perhaps a plot twist is that Naruto's true parentage was hidden because there was a prophecy about him being a threat to the current ninja order. Mikoto and Minato had to keep it a secret to protect Naruto from being killed as a child. But as Naruto grows stronger and starts to show signs of his powerful bloodline, those who fear the prophecy start to target him again. This would force Naruto to not only prove himself but also fight against the unjust system that wants to eliminate him based on a baseless fear.
Perhaps Naruto discovers that his parents' relationship was part of a larger, more secretive plan in the shinobi world. Maybe there was an ancient prophecy that led to Minato and Mikoto getting together to produce Naruto, who is destined for a special role. This could involve Naruto having to face some difficult choices about his identity and purpose. He might have to decide whether to follow the path laid out by this prophecy or create his own.
Naruto would likely be more confident from the start. Since he has the combined blood of Minato and Mikoto, he might not have the same insecurities as in the original story. He would probably be more aware of his potential and be more self - assured in his abilities.
Well, one possibility could be that Naruto has a very different upbringing. Since Mikoto is an Uchiha, Naruto might grow up with a deeper understanding of the Uchiha clan's ways. He could be trained in Uchiha techniques from a young age. Maybe he would have a natural affinity for fire - style jutsu. And he might also face different challenges related to the Uchiha's history and the events that led to their downfall. His relationships with other characters like Sasuke would be very different too. Instead of being rivals in the same way, they could be more like cousins with a shared family heritage to protect.
Well, perhaps the plot could involve Minato having a secret evil plan all along. He could have used Naruto as part of this plan without Naruto knowing. Naruto then starts to notice strange things related to his father. As he digs deeper, he finds out about Minato's true nature. This could lead to Naruto having to choose between following in his father's footsteps (for some strange reason like power) or defying him and becoming a true hero on his own terms. The story could also involve Naruto's friends either turning against him because of his relation to Minato or helping him to overcome this difficult situation.
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.