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 Naruto loses control over his transformation into the Nine - Tailed Fox in a completely unexpected situation. Maybe during a friendly spar with his friends, and this causes them to fear him in a new way. It would add a whole new layer of drama to their relationships.
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.
One possible plot twist could be that Saphira, as a human, has to relearn all her dragon skills in a human form. For example, she might have to find new ways to use her strength or her senses which were so much more powerful as a dragon. Another twist could be that she has to hide her true identity from other humans who might fear or try to use her if they knew she was once a dragon.
A plot twist could be that Akatsuki has a hidden agenda that Naruto, Sasuke and Sakura are unaware of when they join. Maybe Akatsuki is being controlled by an even more powerful and sinister force, and the three are lured in as pawns. They then have to figure out the real situation and fight not only against the Akatsuki members who oppose their reform ideas but also against this hidden power.
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.
Another idea is that Naruto's death while protecting Sakura causes a rift between Sakura and Sasuke. Sasuke might blame Sakura for Naruto's death in some way, either directly or because he feels Naruto wouldn't have been in that situation if it wasn't for Sakura. This could lead to a complex and angsty storyline where Sakura has to deal with the guilt of Naruto's death as well as Sasuke's coldness towards her.
One possible plot twist could be that Orochimaru has a new jutsu that Naruto has to figure out quickly to save Sakura. Maybe it's a jutsu that messes with time, so Naruto has to break through different time loops to reach Sakura. Another could be that Orochimaru has an unexpected ally who tries to stop Naruto from rescuing Sakura. This ally could be someone from Naruto's past who has a grudge against him.
Well, perhaps in the fanfiction, Peter's memories as an adult are still somewhat intact in his baby form. So he tries to communicate with his loved ones in his own baby - like ways, like making specific noises when danger is near or trying to write in a very clumsy way. This could lead to some really cute and interesting interactions.