Maybe in the fanfiction, Sasuke suddenly loses all his powers. Naruto and Neji then have to find a way to restore his powers. But as they search, they find out that the power loss was actually a part of a greater plan by an ancient ninja clan to test the strength of the new generation. This would turn their simple mission into a complex struggle against an unknown enemy.
A great plot twist could be that Neji, who was thought to be a loyal Leaf Village ninja, is actually a spy for an enemy village. This would completely change the dynamics between him, Naruto and Sasuke. They would have to figure out how to deal with this betrayal while also dealing with other threats to the village.
One interesting plot twist could be that Neji discovers a new power within his Byakugan that makes him evenly matched with Naruto's Nine - Tails power. Maybe he unlocks a hidden ability that allows him to see through Naruto's chakra cloaks or disrupt the Nine - Tails' chakra flow. Another plot twist could be that Naruto loses his access to the Nine - Tails' chakra during the fight, and has to rely solely on his own skills and training, making it a much more even match against Neji.
A great plot twist could be that Sai is secretly working for an enemy all along. He has been feeding information about Naruto and Sasuke to this unknown foe. This would completely change the dynamics between the three characters.
A possible plot twist could be that Sasuke's vampire condition was actually a curse placed on him by an old enemy of the Uchiha clan. This would add a whole new layer of mystery and revenge to the story. Another twist could be that Naruto discovers he has some sort of power that can either nullify or enhance Sasuke's vampire abilities. It would put their relationship in a new light as Naruto has to decide what to do with this newfound knowledge.
One idea could be a story where Naruto, Sasuke and Neji are sent on a joint mission to a far - off land. They face many challenges along the way and have to learn to work together better. Neji's Byakugan could help in scouting, Sasuke's powerful jutsu for combat, and Naruto's never - give - up attitude could keep their spirits high.
Maybe they travel back to their early days at the ninja academy. Naruto, who now has all his future knowledge, tries to befriend Sasuke in a different way. But Sasuke, being suspicious, thinks Naruto has some ulterior motive. This leads to a whole new set of comical and at the same time tense interactions between them as they both have to deal with their past selves and the changes they want to make.
A great plot twist could be that Sasuke suddenly loses his sharingan and has to rely on his other skills and the help of the others. Naruto might have to train Sasuke all over again, and Hinata and Sakura could be involved in finding a way to restore Sasuke's sharingan. It would change the dynamics of their relationships and how they interact with each other.
Imagine a fanfiction where Sakura, instead of being in love with Sasuke, has feelings for Naruto all along. This would completely change the love triangle aspect and lead to a lot of interesting interactions between the three main characters. It could also cause Sasuke to re - evaluate his relationship with his teammates.
One plot idea could be a story where Neji, despite his initial doubts, trains Hinata intensively to become a stronger ninja. This could involve them going on a journey to a special training ground and facing various challenges together.
Well, in this kind of fanfiction, a really interesting plot twist could be a time - travel element. Imagine Fem Naruto and Neji are sent back in time to before they even knew each other. They have to find a way to get back to their own time while also not changing the past too much. Another plot twist could be that a strange illness affects only ninja who are married to each other, and they have to find a cure together. Or there could be a situation where a powerful artifact is found that has the power to break their marriage bond if misused, and they have to protect it from falling into the wrong hands.
Another plot twist could be that an enemy uses their relationship against them. The enemy could spread rumors or false information to create chaos and turn the ninja world against them. Naruto and Sasuke would then have to fight not only to protect their relationship but also to clear their names and prove that their love doesn't mean harm to the ninja world.