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.
One possible plotline is that they discover they have a special connection that is related to some ancient ninja prophecy. They then have to go on a journey together to figure out what it means.
In such a fanfic, Naruto might initially be confused when he meets his counterpart. They could compare their lives, skills, and experiences. Maybe they would have a friendly spar to test each other's strength.
In such a fanfic, Naruto might be initially confused by the presence of his female counterpart. They could start by comparing their jutsu skills. Maybe she has a different way of performing the Rasengan, which would be really interesting to see.
One interesting plot twist could be that the alternate Naruto is from a parallel universe where the roles of good and evil are reversed. This would force the real Naruto to question his own beliefs and values. And it might also lead to a battle between the two Narutos, not just a friendly encounter, as they fight over what is right and wrong.
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.
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.
One possible plot development is that Naruto's dad helps him unlock new powers. Maybe he shows Naruto a secret Uzumaki technique.
Maybe the seventh swordsman has a secret power that is unleashed when Naruto is in a dire situation. This power could be something that was thought to be lost or forgotten in the Naruto world, and its appearance changes the entire dynamic of the story.
One possible plot twist could be that Danzo is actually being controlled by an even greater enemy. So, when Naruto is about to defeat him, he realizes that there's a bigger threat behind Danzo. Another could be that Danzo reveals a hidden power that he has been suppressing all along and suddenly becomes much stronger than Naruto expected.
Maybe Naruto discovers that Matatabi has a hidden past that is linked to his own family. For example, his mother or father had a secret encounter with Matatabi before he was born, and this changes the way he views his family and his connection to Matatabi.