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 that Naruto has the ability to control the souls of the dead, inherited from his mother, the Fem Shinigami. This could lead to him being able to communicate with past Hokages in a more direct way than just through their chakra imprints. Another plot twist might be that Naruto has to face an enemy who is also related to the Shinigami realm and his connection to it is the key to victory.
Well, a cool plot twist might be that Fem Naruto has a secret lineage related to Madara's own clan. Maybe she discovers this and it makes Madara question his long - held beliefs and grudges. Or perhaps in the fanfiction, Fem Naruto is able to use a new form of ninjutsu that is a combination of Uzumaki and Uchiha techniques, which she uses to outwit Madara in a crucial battle. It could also be that Madara's real goal was to actually find a successor like Fem Naruto all along and his actions were just a test to see if she was worthy.
Well, the plot might involve Yandere Fem Madara seeing Naruto as the only one worthy of her attention. She could use her powerful abilities to protect Naruto in a very overbearing way. For example, she might attack anyone she perceives as a threat to Naruto, even if they are just his friendly rivals. Naruto, being Naruto, would initially be confused by her extreme behavior but then would try to set things right.
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.
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.
Well, it could be about a female Naruto who has the powerful bloodline of Madara. Maybe she struggles to control the immense power within her while also facing the expectations and fears of those around her. She might have to prove herself in a world that still has remnants of the old grudges from Madara's time.
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.
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.