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.
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.
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.
Maybe in the fanfiction, Madara has a hidden weakness that only Naruto can sense. For example, Naruto might notice that Madara's control over his Sharingan wavers when he's near a certain type of natural energy. So Naruto uses this to his advantage and lures Madara to that area during the fight.
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 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.
Some fanfictions might depict Naruto as having a deeper understanding of the chakra system than ever before. He could have found a way to disrupt Madara's connection to the chakra source, or maybe he was able to use his own chakra in a way that nullified Madara's powerful jutsus. Also, Naruto's experience from all his previous battles might have led him to anticipate Madara's moves and strategies, allowing him to stay one step ahead and ultimately defeat him.
One interesting plot twist could be when a Splatoon character suddenly gains Naruto - like powers. Imagine an Inkling being able to use the Rasengan. It completely changes the dynamic of the story.
A really interesting plot twist can be when the characters from Undertale end up in the Naruto world and they have to adapt to the ninja way. For example, Sans using his shortcuts in the middle of a ninja battle, which throws everyone off guard. It's unexpected and adds a whole new level of humor and chaos to the story.
In some fanfictions, a big plot twist is when Naruto suddenly gains a Devil Fruit ability, completely changing the power dynamics. For example, in 'Naruto's Devil Fruit Adventure', he gets a powerful fruit that makes his ninja skills even more formidable.
One really cool plot twist is when the values of the Naruto universe start to influence the Decepticons in unexpected ways. For example, the concept of friendship and loyalty that Naruto and his friends uphold might start to make some Decepticons question their own motives and allegiances, which leads to a whole new set of conflicts and resolutions in the fanfiction story. This not only adds depth to the story but also makes for a very engaging read as it challenges the typical Decepticon - like behavior we are used to in the original Transformers franchise.