Another possibility is that it's a rogue Shadowhunter. There are always those in the community who don't agree with the way things are going. If Clary's actions or ideas are seen as too radical, this rogue Shadowhunter might try to stop her by injuring her. This could also lead to a story about Clary trying to understand the motives of this attacker and potentially reform them.
A new and powerful rogue ninja could be responsible. This ninja might have a vendetta against Konoha and see Naruto as a symbol of the village, so they target him and use their strong and devious techniques to injure him badly.
The Projectionist might be responsible. As the Projectionist is always lurking around in the dark corners of the studio, it could mistake Bendy for an intruder and attack him. Its large and menacing form could easily cause some serious injuries to Bendy.
It could be an evil magician. They might see Sadie as a threat to their plans, so they try to take her out by attacking her. For example, they could use dark magic to send shadowy creatures after her that would harm her.
It could be a new villain who has emerged. This villain might have a personal vendetta against T Challa and specifically target him to cause harm.
It could be an alternate version of a character from his own universe. For example, an evil version of one of his friends or allies who has turned against him. In some fanfictions, a time - traveler from the future might come back and try to stop Barry from achieving something, and in the process, cause him harm. Also, a group of villains working together could be responsible. They could coordinate their attacks to overpower Barry and injure him.
The Riddler could be responsible. He might set up a series of elaborate and deadly traps throughout Gotham. Batman, in his attempt to solve the riddles and stop the traps from harming innocent people, could end up getting caught in one of them and getting hurt badly. For instance, a trap could involve a collapsing building or a room filled with sharp objects.
Perhaps it was a result of friendly fire or a mistake by an ally. This would add an interesting layer of drama and conflict, especially if there are trust issues that need to be resolved.
One possible plot development could be that her injury leads to a discovery of a new power within her. As she recovers, she realizes she can now do something she couldn't before, like communicate with a different species in the Shadowhunter world. This new ability then becomes crucial in the fight against a new threat that emerges.
It could be a rival agent from another agency. They might see Annie as a threat and want to take her out of the picture.
Sometimes, it could be due to her own actions. Lydia might be overconfident and take risks that she shouldn't. For instance, she could try to perform a very difficult and dangerous magic spell without proper training, and it backfires, causing her to get hurt.