Less of an overall Scooby Doo story per-say; but I've been working on a Velma BDSM story for the past 6 months. https://chyoa.com/story/The-Worst-Night-of-Her-Life.19926
One thing that would perfectly in the Scooby universe centers around the monster costumes. some of those were huge way big enough that two people could easily fit in one. imaging one of the girls getting snatched and put into a bondage restraint inside the costume where the bad guy could make free use of her body while still playing monster.