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 Naruto's illness is a slow - acting poison. As he gets sicker, he starts to have hallucinations of his past battles and the friends he has lost. His friends and the village elders are in a race against time to figure out who poisoned him and find an antidote. His illness also makes him question his own strength and the future of the village he has sworn to protect.
Another scenario could be that they are poisoned by a new, undetectable toxin. As they gradually weaken, they try to find a cure but run out of time. Their deaths would be a great loss, and it could lead to major changes in the political and social structure of the ninja world as everyone copes with their passing.
In such fanfiction, one scenario could be that Naruto's child is abandoned due to his dangerous lifestyle as a ninja. His enemies might target his family, forcing him to send his child away for safety. Another possibility is that the child has some sort of special power that is not understood and feared by the village, leading to its abandonment. Or perhaps Naruto is in a difficult situation where he believes he can't take care of the child properly, like if he's constantly away on missions and has no support system at home.
Well, in some fanfictions of this kind, Naruto could be tortured physically by being chained up and beaten. His captors might also starve him or deprive him of water to weaken him. It could also be that they use some sort of dark magic or forbidden techniques on him that cause extreme pain and discomfort.
One possible scenario could be Naruto being forced into a situation where he has to seem to betray Sakura to protect her from a greater danger. For example, he might be blackmailed by an enemy into staying away from her or acting against her interests.
In some fanfictions, Naruto might punish Sakura for betraying their friendship. For example, he could distance himself from her, making her realize how her actions have hurt him.
Well, in 'naruto gets stabbed fanfiction', it could be that Naruto is exploring a new and dangerous area where he encounters a powerful and hostile ninja. In the heat of the fight, this ninja manages to land a stabbing blow. It might also be that Naruto is weakened due to some prior injury or chakra depletion, making him more vulnerable to being stabbed by a regular enemy. And, there could be a situation where Naruto is under the influence of some sort of genjutsu that impairs his ability to defend himself and thus gets stabbed.
One possible scenario could be Naruto feeling betrayed by the village. Maybe he discovers some dark secrets about the village leadership and decides he can no longer stay. Another could be that he is framed for a crime he didn't commit and is forced to leave to protect himself. Or perhaps he has a vision of a different path for his life that doesn't involve the village.
One possible scenario could be Naruto being poisoned and his friends desperately searching for an antidote. Another might be that he's severely injured in a battle against a powerful new enemy and is on the verge of death, with the village in chaos as they fear losing their hero. Or perhaps he's been affected by some sort of dark jutsu that's slowly draining his life force.
One possible scenario could be that Naruto leaves due to a misunderstanding with Sasuke. Maybe Sasuke says something harsh about Naruto's skills and Naruto, in his pride, decides to leave. Another could be that Naruto feels he's holding the team back in some way and leaves to train on his own in order to become stronger without being a burden. Or perhaps there's a mission gone wrong where Naruto is blamed for something he didn't do, and he leaves out of a sense of unfairness.