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 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.
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.
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.
One possible fanfiction could be where Madara is sealed during the Fourth Great Ninja War in a different way. Maybe instead of being sealed by Hagoromo's chakra, he is sealed by a powerful new jutsu created by Naruto and Sasuke together. This would change the power dynamics in the ninja world significantly as his threat would be eliminated in a more unique manner.
One possible plot twist could be that Naruto, while being trained by Madara, discovers a hidden agenda. Madara might be using Naruto to gain access to some powerful jutsu or artifact. For example, he could be after the Nine - Tails' power within Naruto in a more devious way than initially thought. Another twist could be that Naruto's new godlike abilities attract the attention of other powerful and malevolent forces from different dimensions, forcing him to fight battles he wasn't prepared for. And perhaps, during the training, Naruto uncovers secrets about the Uchiha clan that Madara has been hiding, which changes his perception of the whole situation.
One possible plot twist could be that Naruto has hidden Uchiha powers. Since he's Madara's grandson in this fanfiction, he might suddenly be able to access the Sharingan or other Uchiha abilities in a unique way. Maybe in a fight, instead of relying on his normal Rasengan, he discovers he can use a powerful Uchiha fire - style jutsu that no one expected.
One possible plot twist could be that Naruto, under their training, discovers a new form of chakra that combines the Senju and Uchiha powers in a unique way. This new power might make him a target for other hidden villages who fear his new - found strength.