One possibility is that there's a misunderstanding between Naruto and Karui. Maybe Karui thinks Naruto has something to do with Sasuke's actions that have affected her village. So, in her anger, she attacks Naruto.
Perhaps Karui is on a mission and Naruto gets in the way by accident. She's a tough fighter from her village and doesn't tolerate any interference. So she lashes out at Naruto without fully understanding his intentions. This could lead to Naruto getting beat up as he might not want to fight back right away.
In the fanfiction, it could be that Karui has been influenced by some outside force or false information. She's made to believe that Naruto is a threat. Naruto, being who he is, might not immediately defend himself with full force, which results in him getting beaten up. Also, Karui's fighting style is quite aggressive, and if she catches Naruto off - guard, it's likely he'll end up on the losing side for a while.
Sasuke could be one. Given their complex relationship, there could be a situation where Sasuke's newfound power or different ideology leads him to fight and beat Naruto in a fan - made story.
Well, perhaps Johnny made some mistake that angered Jally's group. Maybe he accidentally insulted Jally or got in the way of something Jally cared about. So Jally, with his friends, decided to teach Johnny a lesson by beating him up.
Maybe it could be about Lincoln getting into a fight with some bullies at school who beat him up because he stands up for someone. Then his family might find out and there's a whole drama about dealing with the bullies and helping Lincoln recover.
He might be confused at first. Naruto is used to being attacked by enemies, but Karui is an ally. So he would wonder what went wrong.
Well, in a lot of these fanfictions, Stiles can get beat up due to his own recklessness. He might be so determined to solve a mystery or help his friends that he doesn't think about the consequences and ends up in a dangerous situation where he is outnumbered and beaten up. Also, there could be miscommunication. Maybe someone thinks he has done something wrong when he actually hasn't, and they take matters into their own hands and beat him up.
In some fanfictions, Naruto might get beat up when facing a powerful new villain who has some unknown jutsu. This could be a villain created by the fanfic writer to test Naruto's limits.
One possible plot could be that Percy is targeted by a group of jealous rivals. Maybe they envy his status or abilities in the story's world. They might ambush him in a secluded place like an alleyway near his school or in a forest he often visits.
One possible reason could be that he's gotten on the wrong side of a powerful client. Maybe he uncovered some shady business deals of the client during a case, and the client decided to take revenge by having him beaten up. Another reason might be related to his past. If some of his old associates from his pre - Harvey days found out he was now working in a high - profile law firm, they could be jealous and target him.
Perhaps the fanfiction keeps rehashing the same tired storylines about Konoha. Naruto might be tired of seeing the same things over and over again, like always focusing on the village's dark secrets in a clichéd way instead of exploring new aspects of Konoha and its people.
In the fanfiction, it might be that Tsunade believes Naruto has become too dangerous. Maybe she's misled by false information about Naruto's new powers being uncontrollable and a threat to the village. So she decides to betray him to protect Konoha from a potential disaster.