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.
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.
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.
There's also a possibility that it's an accident. In the chaos of a battle or a tense situation, a stray bullet from either side could hit Katniss, even if no one actually intended to harm her directly.
It could be a Sith or a Sith - inspired enemy. They are often the ones causing trouble for the Jedi, and shooting Ahsoka would be a way to strike at the Jedi Order.
It could be a rival assassin. They might see Kassandra as a threat to their own reputation or contracts.
It could be a new, inexperienced doctor. Maybe they make a mistake during a surgery that Meredith is involved in, accidentally causing her harm. For example, they might misread a vital sign or use the wrong instrument.
It could be a new and powerful villain who has emerged. This villain might have a special ability that catches Naruto off - guard during a fight, leading to his injury.
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.
There's a possibility that it's an old enemy who has somehow regained power or found a new way to attack. For example, Frieza's family or the Red Ribbon Army if they had some kind of resurgence. They might target Vegeta and Bulma out of revenge or to gain access to Capsule Corp's technology which Bulma controls.