It could be that Akeno is forced by an enemy to target Naruto. She might use her powers to harm him, and Naruto has to find a way to both avoid her attacks and free her from the enemy's control. This would create a complex situation where Naruto has to balance self - defense and saving Akeno.
It could be an evil spirit that has possessed Akeno. This spirit might be using her to get to Naruto because it sees Naruto as a threat to its plans, whatever they may be. So the main antagonist would actually be this hidden spirit.
In some 'Moka hurts Tsukune' fanfiction, it could be that Moka is trying to protect Tsukune from a greater danger, but her actions are misinterpreted by Tsukune as being hurtful. For instance, she might push him away or keep secrets from him in the name of protection, but this actually causes him pain. Another plot could be that Moka is forced to choose between Tsukune and something else she values deeply, and her choice ends up hurting Tsukune.
Maybe in the fanfiction, Yuki hurts Shuichi emotionally. Yuki could say some very cruel words to Shuichi out of jealousy or misunderstanding, which deeply wounds Shuichi's self - esteem and trust in Yuki.
Well, perhaps Demming spreads false rumors about Castle which then affects Castle's reputation both in the writing world and in his detective - helping adventures. Or it could be that Demming tries to physically harm Castle in a fit of rage or envy. There could also be a plot where Demming manipulates situations to make Castle look bad in front of Beckett, causing emotional harm to Castle as he values Beckett's opinion highly.
One possible plot could be that Wonder Woman is under the influence of some sort of mind - control. Maybe a villain has taken over her mind, and she attacks Batman, who is initially confused as to why his ally has turned on him. Another plot could be a difference in their views on how to handle a major threat in Gotham or the DC universe as a whole. Their conflicting approaches lead to a physical altercation where Wonder Woman accidentally hurts Batman.
Another scenario could be in a battle. Naruto might face an opponent who is much stronger than him. In his determination not to give up, he could keep fighting even when he's already injured. He might take hits that are too powerful for him at that moment, like a powerful genjutsu that makes him harm himself unknowingly while trying to break free, or getting caught in a powerful ninjutsu attack that damages his body severely.
One possible scenario could be that Anko is under some sort of mind - control and ends up hurting Naruto accidentally. Maybe she's been influenced by an enemy's jutsu.
There are also fanfictions where Sakura's actions in choosing Sasuke over Naruto in a more hurtful way than in the original series can be explored. She might publicly reject Naruto in a cruel manner, causing him to question his self - worth. Naruto then might go on a journey of self - discovery to prove himself not just to Sakura, but to the whole village.
One possible plotline could be that Naruto somehow ends up in Akeno's world. They meet and at first Akeno is a bit shy around Naruto. Naruto, with his positive attitude, gradually befriends her. They could go on adventures together, like facing some common enemies in Akeno's realm. Naruto's ninja skills would be very useful in such situations.
It's possible that the writer of the fanfiction has given Akeno a backstory or personality trait that directly clashes with Naruto's. Maybe she is extremely arrogant and Naruto, who is humble and believes in everyone's potential, would find that detestable.