One possible plot twist could be that Bowsette turns out to have some sort of connection to Naruto's world that he never expected. Maybe she has a hidden kekkei genkai - like ability that is related to Naruto's ninja powers.
A plot twist might be that Naruto discovers that Bowsette is not what she seems. She could be under a spell or controlled by an enemy, and Naruto has to figure out how to break the control and free her. This would add a layer of mystery and conflict to the story.
In the 'naruto meets nagato fanfiction', a plot twist might be that Nagato fakes his change of heart at first. He could be playing a long - game to deceive Naruto and the Leaf Village. Or perhaps, there is a prophecy that involves both of them, but it has been misinterpreted all along. And when they meet, they start to uncover the real meaning of the prophecy, which changes everything they thought they knew about their fates and the future of the ninja world.
Well, in this fanfiction, Naruto might be really confused by Bowsette's appearance. Maybe he'd initially mistake her for some kind of strange new ninja with a really unique look.
In a 'naruto meets his counterpart fanfic', a plot twist could be that the counterpart seems friendly at first but is secretly working for an enemy. Or perhaps the counterpart is a clone created by an old enemy of Naruto's with a different set of memories. It could also be that the counterpart has a connection to a long - lost part of Naruto's family that he didn't know about, which changes everything he thought he knew about his own identity.
Well, a really interesting plot twist in 'Mario Meets Peach Fanfiction' could be that Mario himself is the one being tricked. Bowser has created a fake Peach to lure Mario into a trap. And while Mario is busy trying to rescue the fake Peach, the real Peach is actually in another location, in even greater danger. Also, there could be a plot twist where the power - ups that Mario usually relies on are actually cursed this time. When he uses them, they cause more harm than good. Maybe the super mushroom makes him too big to fit through the narrow passages he needs to reach Peach. Another possibility is that Peach has fallen in love with someone else in the time she has been captive, and Mario has to deal with this new emotional situation.
A possible plot twist could be that Videl turns out to have some hidden powers herself. It would completely change the dynamic between her and Gohan.
A plot twist might be that Jotaro loses his Stand abilities temporarily and McCree has to protect him. Or perhaps they find out that there's a traitor among the people they thought were their allies in this fanfiction world. This would force them to re - evaluate their situation and who they can trust. Also, it could be that a powerful artifact they were supposed to protect actually has the power to control them, and they have to fight against its influence.
One possible plot twist could be that Cersei pretends to surrender to Daenerys. Daenerys, believing her, takes Cersei into her confidence. But Cersei is actually plotting a big betrayal from within. She could be secretly gathering her remaining forces and planning to assassinate Daenerys when the time is right.
A possible plot twist could be that the dragon is actually a shapeshifter and turns into a human form that Shirou knows. Maybe it's someone he thought was dead.
One possible plot twist could be that the Dursleys are actually under a spell that makes them act so horribly, and Hermione discovers and breaks it. Another could be that Hermione finds out she has some family connection to the Dursleys, which would be a huge shock for everyone.
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.