Another possibility is that it's someone related to a current case she's working on. A family member of a suspect or a person with something to hide might see shooting Brennan as a way to stop the investigation from progressing further.
Maybe it's a jealous rival in the forensic science field. They see Brennan as a threat to their own reputation and success, so they arrange for her to be shot to get her out of the way.
One possible storyline could be that Brennan's friends and colleagues at the Jeffersonian are in a race against time to find the shooter while she is in critical condition in the hospital. They follow every lead, from her past cases to any personal enemies she might have made.
It could be an ex - boyfriend who is jealous of Annie's new relationships. Maybe he couldn't handle seeing her move on.
It could be an old enemy of Chuck's. Maybe someone from his past who has a vendetta against him for something he did before.
Perhaps a mysterious stranger who has some unknown vendetta against the Heartland family. This person could have been lurking around the ranch for a while, waiting for the perfect opportunity to strike. Or it could be someone within the community who has a hidden agenda and sees Amy as an obstacle to their plans.
It could be an old enemy of Ezra. Maybe someone from his past who has a grudge against him for some reason, like a business deal gone wrong or a personal feud.
Well, perhaps a new character introduced in the fanfiction. Maybe a spy from a rival agency who sees Abby as a threat to their mission. Or it could be an associate of a major criminal that the NCIS has been investigating. They might think that by shooting Abby, they can disrupt the investigation. Also, it's possible that it's a person with a personal vendetta against Abby, like someone she unknowingly wronged in the past.
Perhaps it was someone within Toby's own group who had a hidden agenda. A so - called friend who was jealous of Toby or had some ulterior motives that led them to arrange for the shooting. This would add a lot of drama and betrayal to the fanfiction story.
Maybe it's a rival agent who is jealous of Booth's success and popularity within the agency. They might see shooting Booth as a way to get ahead in their career or gain more power within the organization.
Perhaps a new character who has a hidden agenda. Maybe someone who has a connection to a current case Gibbs is working on and doesn't want him to get too close to the truth. This person might be working for a larger criminal organization and sees Gibbs as a threat.
There's a possibility that it's a family member of a criminal she arrested. They might be seeking justice in their own twisted way. They could have been planning the attack for a long time, waiting for the perfect moment to strike when Burgess was most vulnerable. Another suspect could be a corrupt cop from another precinct who doesn't like the way Burgess and her team are cleaning up the streets and cutting into their illegal activities.