A plot twist could be that their brotherhood is part of a grander scheme by an old enemy. Maybe Orochimaru knew about their relation all along and was planning to use it to his advantage. He could have been the one who separated them when they were young and now he wants to use their new - found bond to manipulate them into doing something bad for the village.
Perhaps the plot twist is related to their family's past. Their parents could have been involved in some sort of secret ninja organization or a forbidden jutsu research. And this connection of being brothers leads them to uncover the truth about their family's dark past, which changes their perspective on the ninja world and their place in it.
One possible plot twist could be that they discover their brotherhood in a very unexpected way. For example, during a dangerous mission, Kakashi might get severely injured and in a moment of delirium, he reveals a long - hidden memory that points to their relation. Naruto, being shocked at first, then realizes it explains some of the strange feelings of connection he had towards Kakashi all along.
One possible plot twist could be that Naruto actually steals something from Kakashi that he thought was unimportant, but it turns out to be a key to a hidden jutsu or a secret mission. Another could be that Kakashi knew Naruto was going to pickpocket him all along and let it happen as part of a training exercise. Maybe Naruto pickpockets Kakashi, but then realizes he has to return the item quickly because it's something that Kakashi needs to save the village.
One possible plot twist could be that the pregnancy is not as straightforward as it seems. Maybe there are some hidden powers or curses involved that are affecting the pregnancy. For example, the unborn child could have a special chakra that is attracting enemies.
Maybe a plot twist could involve their family history. There could be a hidden enemy that targeted their family long ago, and now they have to face this threat together. As they dig deeper into their past, they find out secrets that change their view of themselves and their powers. It could also be that their brotherhood is a key to unlocking an ancient prophecy.
One possible plot twist could be that they face opposition from the Hidden Leaf Village. Since same - sex relationships might not be as openly accepted in the traditional ninja world. Another twist could be that they have to go on a dangerous mission together right after getting married, which tests their new relationship. And perhaps there's a secret enemy who wants to break them apart because their union represents a new kind of hope in the village.
Maybe Naruto adopts Kakashi in a post - war scenario where Kakashi has lost his purpose. Naruto, seeing Kakashi's lost state, decides to take him under his wing. As a result, Kakashi starts to learn new jutsus from Naruto and they develop a bond that is more like brothers. This would be a great opportunity to explore their characters in a different dynamic.
A really interesting plot twist could be that female Naruto is actually from an alternate dimension where she and Kakashi are already married. In this new world, things are different, and she has to figure out how to make their relationship work in this dimension too. Plus, there could be a character who is jealous of their union and tries to break them apart by spreading false rumors about Kakashi's past, which female Naruto has to deal with.
One possible plot twist could be that their relationship is initially opposed by the village elders. They might see it as unconventional or worry about how it could affect Naruto's role as a potential Hokage. Another twist could be that an old enemy resurfaces and targets Kakashi to get to Naruto, seeing their marriage as a weakness to exploit.
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.
One possible plot twist could be that Naruto's love for Kakashi from the past disrupts the timeline. Maybe his feelings cause him to unknowingly change events that were supposed to happen. For example, he might prevent Kakashi from making a certain decision that was crucial in the original timeline.
One possible plot twist could be that Kakashi discovers Naruto has a hidden power that no one else is aware of. This could change the whole dynamic of their relationship. Maybe it's a new type of chakra that only Kakashi can help him control.