It could be a new villain. A powerful and unknown enemy might target Sakura because of her skills or her connection to other important characters. This villain could have a vendetta against her specifically or be trying to send a message to her friends.
Perhaps an accident caused by one of her own friends in a moment of miscalculation. For instance, during a joint training exercise, someone's jutsu goes wrong and accidentally injures Sakura. This would lead to a lot of guilt and self - reflection among the characters.
It could be one of his business rivals in the underworld. They might see Ciel as a threat to their operations and decide to take him out by injuring him. Maybe a new competitor who wants to take over Ciel's territory and influence.
Maybe it's one of his old enemies who has found a new way to attack him. For instance, Vlad could come up with a more devious plan that manages to catch Danny off - guard and injure him. Vlad has always been a formidable foe, and he might use Danny's overconfidence or a moment of weakness against him.
In the fanfiction, it might be a new character introduced specifically for this plot. This new person could be jealous of the Hardy Boys' reputation and wants to harm them. So, they target Joe and cause his injury. Another possibility is that it's an accident caused by a person who didn't mean to harm Joe but was just being careless, like someone working on a construction site near where the Hardy Boys were investigating.
It could be Sasuke. If Sasuke has some sort of newfound connection with Naruto and it causes Naruto to shift his focus away from Sakura, then Sasuke would be the cause. For example, if Sasuke and Naruto team up for a powerful mission and their bond deepens in a way that makes Naruto neglect his relationship with Sakura.
For Kakashi, a character like Naruto could potentially cause jealousy in some fanfictions. Since Naruto and Sakura are very close friends, if Sakura spends a lot of time with Naruto on a mission or training, Kakashi might feel a twinge of jealousy. He might wonder if there are deeper feelings between them. As for Sakura, a new female sensei in the village could make her jealous. If this sensei is very attractive and Kakashi seems to respect her a great deal, Sakura could start to feel envious.
A vengeful god could be the cause. For example, if Percy somehow angered Ares, Ares could manipulate the situation so that Percy gets arrested by mortals. He might use his influence to make it seem like Percy was involved in some sort of illegal fighting or destruction.
It could be Giovanni. If Giovanni gives an order that Meowth finds completely unacceptable, like harming innocent Pokemon for no good reason. Meowth, having a soft heart deep down, might not be able to go along with it and thus betray Team Rocket.
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.
Maybe it's about protecting Sakura. Itachi might think that Sasuke isn't the right person for Sakura and wants to protect her from Sasuke's darker side. And Sasuke, on the other hand, believes he can protect Sakura better than Itachi and that Itachi has no right to interfere.
Another possibility is that she contracted a rare disease while on a medical mission in a far - off land. Since she is a medical ninja, she might be exposed to various unknown pathogens. This could have led to her falling ill and being in the hospital.