One possible scenario could be in a great battle against an extremely powerful enemy. Maybe Naruto uses up all his chakra trying to protect the village from a huge threat like a new and terrifying Akatsuki-like organization. His body just gives out from the overexertion.
Another idea is that Naruto sacrifices himself to seal away a great evil. Similar to how his father sealed the Nine - Tails into him, he might use some powerful sealing jutsu on a huge and dangerous entity. But the cost of this jutsu is his own life.
In a fanfiction of Naruto dying of a sickness, perhaps the sickness is a result of overusing his chakra during a great battle. His body starts to break down, and he begins to experience weakness and fainting spells. Hinata, being his wife, is desperate to find a way to save him. She might turn to her own clan's secrets in hopes of finding a cure. At the same time, Naruto tries to train Boruto in what little time he has left, passing on his values and skills, while also coming to terms with the fact that he won't be there to see his son grow up fully.
Well, it could be a situation where Hinata is trying to protect someone else from Naruto, perhaps believing he is a threat at that moment due to some false information. She might then end up hurting him while trying to fend him off. Or, in a darker fanfiction, there could be an alternate universe where Hinata has turned evil and deliberately targets Naruto to cause him harm.
One possible scenario could be that Kushina's spirit somehow manifests and guides Naruto in a difficult battle. She might use her chakra to give him an extra boost or share some long - forgotten family jutsu with him. Another scenario could be that in a time - travel fanfic, Kushina actually gets to be there in person to save Naruto from a dangerous situation in his childhood that he originally faced alone, like the time he was ostracized in the village as a child.
One possible scenario could be that Kin is captured by an enemy during a battle. Naruto, with his strong sense of justice and his never - give - up attitude, would track her down. He might use his shadow clone jutsu to create distractions and then use his Rasengan to break through any barriers or defenses set up by the captors. Another possibility is that Kin is in a dangerous situation in a different village, and Naruto goes on a diplomatic mission to save her while also trying to improve relations between the two villages.
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.
One possible scenario could be that Sakura is feeling down because she failed a difficult medical ninjutsu exam. Naruto, being the good friend he is, takes her out for her favorite ramen and tells her stories of his own numerous failures and how he never gave up. This cheers her up as she realizes that failure is just a stepping stone to success.
In a battle situation where they are on opposite sides, perhaps due to a misunderstanding or some kind of mind - control. Kakashi, with his superior skills, could accidentally harm Naruto while trying to subdue him. For example, if Naruto is being influenced by an enemy's genjutsu and attacks Kakashi, Kakashi might have to use a more forceful defensive move that ends up hurting Naruto.
Well, Naruto might be hurt in a fanfiction when Team 7 fails to support him in a crucial moment. Let's say Naruto is facing a powerful enemy and he expects his team to have his back. But Sasuke is too preoccupied with his own goals, Sakura is too scared to act, and Kakashi is not around. This feeling of being let down by the people he trusts the most would be a huge blow to Naruto. Another situation could be that Team 7 makes a decision that goes against Naruto's beliefs. For example, they side with a group that Naruto believes is wrong. This would not only make Naruto feel betrayed but also question his place within the team.
One possible scenario could be during a training session. Tsunade, known for her tough training methods, might accidentally go too far and physically harm Naruto while trying to push him to his limits. For example, she could miscalculate the force of a punch during a sparring exercise.
One possible storyline could be that in a major battle against a powerful enemy, Hinata jumps in front of Naruto to take a fatal blow meant for him. This could lead to Naruto going into a rage and unlocking a new level of power in his grief. He might then defeat the enemy single - handedly, vowing to carry on Hinata's will.