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.
Well, it could be that Naruto has a different view on the ninja clans. Female Madara might instill in him a sense of distrust towards the other clans. Maybe she tells him stories of how the Uchiha were wronged in the past, which makes Naruto more protective of the Uchiha and less inclined to cooperate with clans like the Hyuga or the Nara. Also, his fighting style could be a blend of his own natural exuberance and Madara's strategic and powerful techniques. He might learn some unique jutsu that are passed down from Madara's family or knowledge.
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 due to Zabuza's influence, the female Naruto becomes more of an assassin - type. She might develop a different set of values compared to the original Naruto. For example, she could be more ruthless in combat and less hesitant to take lives when necessary.
One possible plot twist could be that the female Kyuubi imparts unique jutsu knowledge to Naruto that no one else in the village has. This could make Naruto a target of envy and suspicion among his peers at first. Another plot twist might be that the female Kyuubi has a hidden agenda related to an ancient prophecy that Naruto unknowingly is a part of. This could lead to Naruto being forced to make difficult choices between his loyalty to the village and the Kyuubi's plan.
A major plot twist could be her forging alliances within the Akatsuki that change the whole power dynamic in the ninja world. She could convince some of the members to turn against the more evil - minded ones in the group. This would not only create internal conflict within the Akatsuki but also change the way Konoha and other villages view her. Instead of seeing her as a potential traitor for being associated with the Akatsuki, they might start to see her as a key figure in bringing down the more dangerous elements of the organization.
Well, it could be that Naruto's relationship with the other Konoha ninjas changes drastically. They might see him as an outcast because of his association with Kisame. On the other hand, Naruto might try to bridge the gap between Konoha and the Akatsuki due to his upbringing by Kisame. This would create a whole new set of conflicts and alliances within the Naruto universe.
One possible plot twist could be that Naruto develops a much darker and more ruthless side due to Zabuza's influence. Instead of the optimistic and friendly Naruto we know, he might be more solitary and calculating in his approach to battles and relationships. For example, he could be more willing to use underhanded tactics like Zabuza's use of hidden mist jutsu to ambush opponents.
One possible plot twist could be that Naruto inherits Hashirama's unique Wood Style jutsu much earlier and in a more powerful form. Since Hashirama was a master of this powerful ability, he might train Naruto intensively in it. This would make Naruto stand out even more in the ninja world and perhaps change the way his peers and enemies view him.
One possible plot twist could be that Naruto gains unique fire - related powers from the phoenix. Since the phoenix is often associated with fire in many mythologies, Naruto might be able to control a different kind of fire jutsu, which would set him apart from his normal abilities in the original Naruto story.
Perhaps Naruto's relationship with the other ninja in Konoha is affected. Since Yoruichi has a different set of values and skills compared to the traditional Konoha ninja, Naruto could be seen as an outlier. This could lead to some initial misunderstandings and later, a new form of respect from his peers as they see the effectiveness of his unique upbringing.
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.