Perhaps in this fanfiction, Naruto is possessed by some dark force that makes him act out of character and become a threat to the village. Sakura, being the strong - willed and skilled kunoichi she is, has to beat him up in order to subdue him and try to find a way to free him from the dark influence. This would make for an action - packed and emotionally charged plot.
Maybe Sakura gets angry at Naruto for some misunderstanding, like he accidentally ruins one of her important medical experiments. So she decides to beat him up to teach him a lesson.
One possible reason could be a misunderstanding. Maybe Sakura makes a decision that Naruto strongly disagrees with regarding the safety of the village or their friends. For example, if Sakura decides to trust an enemy without Naruto's knowledge, Naruto might get so angry that he lashes out at her.
Well, in such a fanfiction, perhaps Sasuke has some sort of plan that involves Hinata in a negative way. Naruto discovers this and decides to beat up Sasuke to protect Hinata. It could also be part of a bigger struggle where Sasuke's actions are seen as a threat to the future Naruto envisions with Hinata, so Naruto takes matters into his own hands to stop him.
Maybe Sasuke says something really offensive about their past or her skills, and Sakura just snaps and starts beating him up.
A fan who really likes Sakura and wants to show her strength. They might be tired of seeing Sakura always in a support role and want to create a scenario where she takes the lead and shows her power by beating up Naruto.
One possible reason could be a simple rivalry that has boiled over. Maybe they were competing for the same mission, and Naruto's determination to prove himself got the better of him. He might have seen Kiba as a threat to his goal of becoming Hokage, thinking that if Kiba succeeds in a high - profile mission, it could overshadow his own achievements.
In this fanfiction, perhaps there is a misunderstanding between Luke and Percy. Luke might think Percy has betrayed him in some way, like siding with the wrong people in the context of their fictional world, and thus resorts to violence by beating him up.
Perhaps in the fanfiction, Percy is under some sort of dark influence. This could be from a new, unknown magical force. This influence makes him see Jason as a threat to his friends or himself, so he attacks Jason. Jason, on the other hand, is initially confused but then tries to fight back to defend himself while also trying to figure out what's wrong with Percy.
Sasuke would likely be very conflicted. On one hand, he has his own relationship with Naruto and Sakura. He might initially be angry at Naruto for attacking Sakura. But if he discovers the reasons behind it, he may understand Naruto's actions to some extent.
Perhaps in this fanfiction, his sister has done something wrong or dangerous, and Naruto has to 'beat' her in the sense of stopping her. It could involve a moral or ethical conflict within the story that Naruto has to resolve by overpowering his sister's actions.
One common theme is competition. Naruto and Sakura are often shown competing in some form, like a ninja battle or a test at the academy, and Naruto comes out on top. Another theme could be growth. Naruto's victory over Sakura might be a catalyst for her to grow and improve herself. Also, friendship is sometimes a theme. Even though Naruto beats Sakura, it doesn't damage their friendship but rather strengthens it in some way.