One possible scenario in such a fanfiction could be that Sirius is somehow forced or tricked into becoming a Death Eater. Hermione might then try to rescue him from the dark side. Maybe she discovers some ancient magic that can reverse the dark mark's influence on him.
In this fanfiction, Hermione could initially be in denial about Sirius being a Death Eater. She might think it's a ploy by Voldemort to mislead the Order of the Phoenix. So, she starts her own investigation, using her vast knowledge of magic and her sharp intellect to get to the bottom of it.
A great plot point could be that Sirius, as a Death Eater, is given a mission to target Hermione. But when he faces her, he can't bring himself to harm her because of their previous relationship. This internal struggle within Sirius and Hermione's attempts to bring him back to the light could form the core of the fanfiction.