It might be a jealous rival. If Sakura is popular or has something that others envy, like a special talent or a relationship, a rival could have stabbed her out of envy.
Well, in some 'Peter Parker Gets Stabbed' fanfiction, it might happen during a fight with a new, powerful villain. The villain could have a weapon specifically designed to harm Spider - Man, like a blade coated with a substance that weakens his healing factor. Peter might get stabbed while trying to protect someone, like MJ or Aunt May. And then he has to deal with the injury, hiding it from his loved ones while also trying to figure out how to defeat the villain before the wound becomes too much to handle.
Perhaps Sakura's injury makes her realize she has some hidden strength within her. She could start to have visions or gain new abilities while she's recovering from the stabbing. This could then lead to a whole new arc in the fanfiction where she has to learn to control these new powers.
One possible plot development could be that Naruto's friends rally around him to protect him while he recovers. They might seek revenge on the one who stabbed him.
Maybe it's an enemy from another village who sees Naruto as a threat to their plans. For example, if there's a group in another village that wants to start a war, they might think that getting rid of Naruto would give them an advantage. Another possibility is that it's a character who has been brainwashed or controlled by an evil force. This could add an interesting layer to the story as Naruto's friends would have to not only deal with his injury but also find a way to break the control on the stabber.
The stabbing of Clary can completely shift the direction of the fanfiction. It can create alliances that were not there before. Other characters might put aside their differences to find out who stabbed Clary and why. It can also introduce new elements to the story, like a new weapon or a new type of magic that is needed to heal Clary. Plus, it can heighten the tension between different groups, such as the Downworlders and the Shadowhunters, if there is suspicion among them regarding the stabbing.
Another possibility is a character who has been possessed by an evil spirit. They may not be in their right mind when they stab Merlin. This could add an element of mystery as Merlin has to figure out not only who stabbed him but also how to exorcise the spirit from the person's body.
Well, it could lead to a major shift in the story's direction. Maybe Tony's friends would react differently and it could change the whole plot dynamic.
Chuuya is not dead in the manga. The author has kept him alive to drive the story forward and create interesting developments. His presence adds a lot of excitement and intrigue to the plot.