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.
In some fanfictions, Naruto could also hurt himself because of his own self - doubts. He might think that he's not good enough to protect his friends or the village. So, he could engage in extreme self - training regimes that are harmful. For instance, he could be doing excessive physical exercises without proper supervision or using his chakra in ways that are dangerous to his own body in an attempt to become stronger quickly.
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.
Well, it's possible that in the fanfiction, Naruto is experimented on as part of a desperate attempt to save the village. There could be a new threat on the horizon, and the village elders or some ninja with knowledge of forbidden techniques believe that by experimenting on Naruto, who has shown great resilience, they can find a solution. They might be trying to turn him into a weapon or a shield for the village, which would put Naruto in a really tough situation both physically and morally.
One possible scenario could be Naruto exploring new jutsu by experimenting on his own chakra. Maybe he tries to combine different elemental chakra within himself in unorthodox ways to create a super powerful and unique jutsu. Another could be related to his physical endurance. He might experiment with training methods that push his body to the limit, like enduring extreme pain or fasting for long periods while still trying to perform at his best in combat simulations.
One possible scenario could be a misunderstanding between Pike and Burnham that leads to emotional hurt. Maybe Pike makes a decision in a mission that Burnham disagrees with strongly, and it causes a rift between them.
Often, in fanfictions, power struggles can lead to Boruto hurting Naruto. If Boruto becomes too power - hungry and Naruto tries to stop him from going down a wrong path, Boruto might see it as Naruto trying to keep him weak. This can lead to conflict between them. Also, there are times when Boruto blames Naruto for the death of someone close to him (even if it's not Naruto's fault), and in his anger, he hurts Naruto.
One possible scenario is that she's trying to protect the Candy Kingdom from a new threat and Finn's impulsive actions get in the way. So, in her attempt to stop him from endangering the kingdom, she might accidentally hurt him. Another could be that she's under the influence of some sort of mind - controlling substance or magic and she ends up harming Finn without realizing it.
Maybe Naruto's illness is a result of some dark jutsu used against him. His illness could lead to him being unable to perform his ninja duties, and so his friends, like Sasuke and Sakura, have to take on extra missions to protect the village while also trying to find a way to heal him. They could search through ancient ninja scrolls for a remedy.
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.
One possible scenario could be that Vegeta is too focused on his training and ignores Bulma's emotional needs. He might be constantly pushing himself to get stronger and in the process, not give Bulma the attention she desires. For example, he could skip out on family events or important dates just to train.
One possible scenario is when Artemis criticizes Percy's fighting style. Percy has his own way of battling monsters, which is effective but might not be as refined as the way the hunters of Artemis do it. If Artemis were to publicly criticize his style in front of others, it would surely wound Percy's feelings. He might feel like he is not good enough in her eyes.