Well, a great plot development could be that the shooting was part of a bigger conspiracy against the BAU. Maybe someone is trying to take down the whole team and Hotch was just the first target. This would lead to the team having to dig deep into past cases to figure out who has a vendetta against them. Also, Hotch's family could be brought into the story more. His son might be scared for his father's life and this could add an emotional layer to the fanfiction.
In some fanfictions, the shooting of Hotch could lead to a new character being introduced. This new character could be a doctor who has a special connection with Hotch during his recovery. Their relationship could develop into something more than just patient - doctor. Or, the shooting could be a way to explore Hotch's past traumas more deeply. He might have flashbacks to other dangerous situations he's been in, and this could help him grow as a character while he's recovering.