It could be an enemy ninja from another village who wants to take out Konoha's strongest shinobi. Maybe someone from the Sound Village still holding a grudge against Naruto.
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.
It could be a powerful Hollows or Arrancar. Since they are often the antagonists in the Bleach universe, they might see Naruto as an intruder or a threat to their plans. Maybe a powerful Hollow with a thirst for powerful souls targets Naruto, thinking his unique chakra would be a great addition to its power.
Maybe it's a new villain who is trying to make a name for themselves. This villain could see shooting Captain America as a way to gain instant notoriety in the criminal underworld. They might have studied Captain America's weaknesses and found an opportune moment to strike.
It could be an old enemy seeking revenge. Maybe a powerful Titan who escaped Tartarus and blames Percy for his previous defeat. This Titan could have been plotting in secret, waiting for the perfect moment to strike and finally end Percy's life.
It could be a rogue ninja from a neighboring village. Maybe they were hired by a shadowy organization that wanted to disrupt the balance of power. This ninja might have been specifically targeting Naruto because of his status as a hero and a symbol of hope for the Hidden Leaf Village.
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.
Kakashi Sensei could also be involved. He is Naruto's teacher and mentor. If Naruto gets hurt during a mission that Kakashi is leading, Kakashi would surely be there. He might feel responsible for Naruto's injury and would do everything he can to protect him further and get him to safety. And then there's Pain. In some fanfics, Pain could be the one who attacks Naruto and causes him to get hurt, especially if the fanfic is centered around the events related to Pain's invasion.
Obviously Naruto himself is the central character as the story is about him getting disowned. His friends like Sasuke and Sakura might also be involved. Sasuke could be conflicted between his loyalty to the village and his friendship with Naruto. Sakura might initially be confused about whether to side with the village or Naruto. And then there are the village elders like Danzo who could be the ones behind Naruto's disownment in the fanfic.
It could be an old enemy of Nicole's from her police work. Maybe someone she put in jail before who has a vendetta against her. This person might have been released recently and is out for revenge.
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.