In the 'naruto is madara pet' fanfiction, a really unexpected plot twist could be that the entire concept of Naruto being Madara's pet was an illusion created by an even greater enemy. Another plot twist could be that Naruto's pet status gives him access to a secret power or knowledge that Madara has been hiding. And maybe, as Naruto becomes more and more involved in Madara's life as a pet, he starts to influence Madara's decisions in a way that leads to a completely different future for the ninja world than what was expected.
Well, a plot twist might be that Naruto's friends come to rescue him but when they do, Naruto refuses to leave because he has uncovered some truth about Madara or the situation that he believes is more important than his freedom. Also, it could be that Madara has a change of heart and decides to sacrifice himself for Naruto, completely changing the dynamic of their relationship from master - pet to something more selfless. And there could be a plot twist where Naruto turns out to be a reincarnation of someone important to Madara's past, which makes their relationship even more complicated.
One possible plot twist could be that Naruto actually allows himself to be captured on purpose. He might have a secret plan to infiltrate Madara's stronghold from the inside and gather intelligence. Another twist could be that Madara discovers a hidden power within Naruto that he wasn't expecting, and this power either scares him or makes him change his plans completely.
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.
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.
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.
In some fanfictions, there could be a plot twist where Madara and Naruto end up switching sides for a brief moment. Maybe Madara sees the error of his ways due to Naruto's unwavering belief in friendship and peace, and he helps Naruto defeat an oncoming threat, only to then go back to being the antagonist. Or perhaps Naruto discovers that he has a hidden connection to Madara's past, something that changes the whole dynamic of their battle and leads to Madara's defeat in a very unexpected way.
One common plot twist could be that Madara had his memories wiped and didn't know about Naruto being his son until some fateful encounter. Another might be that Naruto's mother was part of a secret mission involving Madara.
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 interesting plot twist could be that female Naruto, with her knowledge of the future, tries to prevent Madara from making certain mistakes that led to his downfall in the original timeline. For example, she might show him the true nature of the power he was seeking, making him question his motives.
Perhaps Naruto discovers that Sheele was sent to his world by an enemy as a spy, but she has actually fallen in love with the place and the people, especially Naruto, and she has to prove her loyalty. This would create a lot of drama and tension in the story.