Perhaps a plot twist could be that Naruto and Madara's mother was from a powerful and secret clan. This clan has a prophecy about two brothers saving or destroying the shinobi world. Naruto and Madara are unaware of this prophecy until later in the story. As they start to discover their true potential together, they realize that they have a choice to make. This could lead to internal struggles within each of them as they decide whether to fulfill the 'saving' part of the prophecy or be swayed by Madara's past desires for power and destruction. It would add a layer of mystery and moral dilemma to the fanfiction.
One possible plot twist could be that Naruto, after becoming a Madara fan, starts to question the traditional values of Konoha. He might see Madara's vision of a more unified world under his rule as something appealing. This could lead to a rift between him and his friends as they struggle to understand his new perspective.
Well, one possible plot twist could be that Madara's reason for saving Naruto is not entirely selfless. Maybe he has a hidden agenda related to some ancient prophecy in the Naruto universe. He might see Naruto as a key to achieving something greater for himself or his clan.
One possible plot twist could be that Naruto's values are very different from the original. Since he's raised by Female Madara, he might have a more aggressive approach to achieving peace. For example, he could be more willing to use forceful means rather than the diplomatic ways he often tries in the original story.
In this fanfiction, a plot twist could be that the seal actually has a secondary effect. Instead of just containing Madara, it also starts to absorb some of his power into Naruto. So Naruto gradually becomes stronger in a very unorthodox way. However, this also comes with risks as the power of Madara might corrupt Naruto's mind. Also, there could be a group of ninjas who believe that Naruto should be killed to ensure Madara is never released. This would put Naruto in a difficult situation where he has to fight not only against the possible corruption within him but also against those who see him as a threat because of Madara's presence inside him.
One possible plot twist could be that while wearing the Madara armor, Naruto gains some of Madara's combat skills and memories. This makes him question his own identity and purpose. He might start to see things from Madara's perspective, which could lead to conflicts within his team as they don't understand his sudden changes.
Perhaps a plot twist could be that the village initially rejects Naruto due to his relation to Fem Madara. They fear he might turn out like his mother and bring destruction. This would force Naruto to prove himself in a different way than in the original series. He might have to find allies outside the village and then come back to redeem himself in the eyes of the villagers.
One possible plot twist could be Naruto facing discrimination within the noble circles due to her status as the Daimyo's daughter but also being a female ninja. Another could be political intrigue where her position is used by enemies of the Daimyo to gain power. For example, they might try to kidnap her to force the Daimyo into making concessions.
One interesting plot twist could be that they discover their twin bond gives them shared magical abilities that are unique. For example, they might be able to combine their powers to create a new kind of spell.
Maybe a plot twist could involve their family history. There could be a hidden enemy that targeted their family long ago, and now they have to face this threat together. As they dig deeper into their past, they find out secrets that change their view of themselves and their powers. It could also be that their brotherhood is a key to unlocking an ancient prophecy.
Perhaps Madara fakes his death in the fanfiction after meeting Naruto. Naruto then has to deal with the chaos that follows as Madara secretly manipulates events from the shadows. Or, it could be that Naruto's presence causes Madara to have a change of heart, but then the ninja world doesn't believe that Madara has truly changed and they both have to fight against the world's distrust. There are so many ways the plot can take an unexpected turn in this kind of fanfiction.