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.
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.
I'm not sure specifically as there could be many different interpretations in such a fanfiction. It might involve a character named Rito facing a stabbing incident, perhaps in a battle, a crime scene, or a situation of betrayal.
It could be a rogue angel. There are always some angels in the Supernatural universe who oppose Castiel's ideas or actions, and they might see stabbing him as a way to get rid of him or send a message.
In such fanfiction, characters might show shock. For example, Dean could be horrified when he sees Castiel stabbed, his eyes wide open and his face pale.
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.
Perhaps he gets stabbed as a part of a plot to take over his company. His rivals could be behind it, seeing his success as a threat. In the fanfiction, this could lead to a great revenge story where Kaiba has to regain his power and seek justice.
A new student in the school could be the one to save Sakura. This new student might have had similar experiences in their previous school and decides to take a stand against the bullies when they see Sakura being harassed.
Sakura could use her medical ninjutsu skills to create a distraction. For instance, she might make it seem like she's poisoned herself, causing Sasuke (or whoever is involved in the kidnapping) to get closer, and then she could attack and escape.