One possible plot twist could be that Naruto and Sakura are forced to betray their village under some kind of mind - control. Maybe an enemy has a powerful jutsu that can manipulate their thoughts and actions. So, they end up doing things that seem like a betrayal to their friends and comrades.
Another idea is that they discover some dark secrets about the village that make them feel betrayed first. For example, if they find out that the village leaders have been using unethical means for power. In response, their actions are misinterpreted as betrayal when in fact they are trying to expose the truth. This could lead to a lot of conflict and drama in the fanfiction.
Another reason might be due to a personal vendetta against someone in the village. If someone in the village wronged them deeply, like a powerful figure who abused their power, Naruto and Sakura might take actions that seem like betrayal to the village in order to seek justice. However, they would likely believe they are doing the right thing in the long run.
The plot of a Naruto turns into Sakura fanfiction could involve Naruto experiencing Sakura's emotions more directly. He might feel the pressure she has always felt to keep up with Naruto and Sasuke. This could lead to him understanding her better and trying to change things when he turns back. Also, there could be a situation where Naruto - as - Sakura has to go on a mission alone. This would force him to fully embrace Sakura's skills and personality. He could end up using her intelligence and strategic thinking in ways he never thought possible, which would not only be a growth for the 'Naruto - in - Sakura' character but also an interesting exploration of Sakura's potential.
One possible plot twist could be that right before the wedding, Naruto has to go on a dangerous mission. This could put their relationship to the test as Sakura has to deal with the fear of losing him. She might even consider calling off the wedding. Another plot twist could be that an old enemy resurfaces and tries to use Sakura as a leverage against Naruto, forcing him to make a difficult choice between his love and the safety of the village.
One possible plot twist could be that they run off to a hidden village that is not known to the main ninja world. There, they discover a new type of chakra that has the power to heal any wound and bring back the dead. But this new power also has a dark side that attracts the wrong kind of attention from other ninja clans.
One possible plot could be that Naruto and Temari are forced to betray their respective villages due to some false accusations. Maybe an enemy manages to frame them for a crime they didn't commit, like stealing a powerful and dangerous jutsu scroll from their villages. In order to clear their names and protect their loved ones from the wrath of their villages, they go on the run together. Along the way, they discover the real mastermind behind the false accusations and have to fight against this powerful enemy while also trying to convince their villages of their innocence.
Another interesting plot twist could be related to the purpose of Naruto's transformation. Suppose Naruto transforms to save Sakura from a dangerous situation. But the transformation has some unforeseen side effects. For instance, he might lose control of his new powers temporarily. Sakura then has to find a way to help him regain control while also dealing with the threat that made him transform in the first place.
Well, they might join Akatsuki in fanfiction because they think they can change the organization from the inside. Naruto, with his strong belief in redemption, could believe that he can turn the Akatsuki members to the good side. Sakura, who always stands by Naruto, would follow him. Once inside, they would face a lot of challenges. The Akatsuki members are all very powerful and have their own motives. Naruto and Sakura would have to deal with the likes of Itachi and Kisame. Itachi might see through their plan, or they might actually start to understand Itachi's own complex situation and motives which could lead to a whole new set of developments in the story.
A plot twist could be that Naruto and Sakura get married in an alternate universe where things are different from the original Naruto storyline. Maybe in this universe, Sasuke never left the village, and Naruto and Sakura developed feelings for each other over time while working on missions together. Their marriage could then be a symbol of a new era of peace and cooperation in the village. However, they soon discover that there are dark forces at work trying to undermine their relationship and the stability of the village.
A plot twist could be that Sakura and Hinata actually team up against Naruto in some way. Perhaps they realize that Naruto is being pushed into a relationship by the village elders for political reasons. So, they decide to fake a relationship between themselves to make Naruto see that he should be free to choose his own path and not be pressured into a marriage. This would turn the typical love triangle on its head.
A plot twist could be that Naruto suddenly loses his ninja powers right before the wedding. This would create a huge dilemma as he is seen as a hero in Konoha. Sakura would then have to decide if she still wants to marry him without his powers. Also, perhaps a new character shows up claiming to be Naruto's long - lost brother and tries to stop the wedding because he has some grudge against their family.