It could be Sasuke. If Sasuke completely rejects Naruto's friendship and the idea of coming back to the village, Naruto might be deeply hurt. He has always been trying to bring Sasuke back, and if Sasuke shuts him out completely, it could be a major factor in his downward spiral.
The villagers themselves might be the cause. Even though Naruto has proven himself to them, if they suddenly turn on him again and reject him due to some false rumors or misunderstandings, it would be a huge blow. Naruto has always wanted their acceptance, and this rejection could break his spirit and lead to his dying state.
It might be his sensei, like Kakashi. If Kakashi for some reason rejects Naruto, maybe because of some tough decision he has to make that Naruto doesn't understand. Naruto respects Kakashi a great deal, and this rejection from his teacher could make him lose faith in himself and the path he's on, ultimately leading to his death due to the emotional rejection.
In such a fanfiction, Naruto might be rejected by his friends or the village. This could lead to a deep sense of despair and loneliness. His chakra might be affected, and he could gradually lose his will to live. Maybe he'll stop eating or training, and his physical condition will deteriorate until he's on the verge of death.
It could be a new villain. Maybe a villain who targets Naruto's loved ones and Naruto is unable to save them. This failure would cause him great heartbreak. For instance, if the villain kidnapped Hinata and Naruto couldn't rescue her in time.
Sasuke could be a great main character in such a fanfiction. He has a deep connection with Naruto. If Naruto's dying will flame is involved, Sasuke might be on a journey to understand what Naruto left behind and how to carry on his legacy. He could be conflicted between his own past and the new responsibility that comes with the dying will flame.
It could be a genjutsu cast by an unknown enemy. This enemy might be targeting Naruto specifically to make him vulnerable. They could be using sleep paralysis as a way to weaken his mental state before a bigger attack.
It could be a rogue shinobi from Naruto's past who has been biding his time. This shinobi might have developed a new jutsu specifically designed to target Naruto and make him die slowly. He's doing it secretly to cause chaos in the Hidden Leaf when their hero suddenly passes away.
Another character could be Kakashi. Maybe he has to make a tough decision that goes against Fem Naruto's wishes. For example, not allowing her to go on a dangerous mission she really wants to. This could make Fem Naruto feel betrayed and heartbroken, as Kakashi is a respected figure in her life.
Perhaps Naruto has had some negative experiences or premonitions related to the toads. Maybe he saw something in a dream or heard a story that made him hesitant about entering into the contract. Another aspect could be that he wants to break away from the traditional paths of the ninja in his village and forging a new way without the toad contract is part of that.
One possible reason could be that their worlds and values are too different. Naruto is from the Hidden Leaf Village with its own set of ninja ethics and goals. Rias, on the other hand, is from a different fictional universe with her own set of rules regarding devils and their society. Maybe Naruto's straightforward and often self - sacrificing nature doesn't align with what Rias expects in her world.
: Sasuke could be a possible cause, not out of malice but maybe during an intense fight where things get out of control. They have had some really rough battles, and in the heat of the moment, Sasuke could accidentally use a technique that affects Naruto's ability to breathe. Also, there could be some new villain in the fanfiction that we don't know about yet, who has a specific grudge against Naruto and targets his breathing as a way to weaken him.
It could be an old enemy who has come back with new and more terrifying powers. For instance, Orochimaru might return with some kind of jutsu that can directly target Naruto's mind and create unfathomable fears in him.