I'm working on a story module for this that is kind of Murder She Wrote meets Silent Hill. I have two story tones going on, a lighter whodunnity one for when players are interacting with NPCs, and a darker psych horror one for when they deal with the darkness directly.
The manifestation of the darkness can be warded against and made invisible by people untouched by it. I'm adding mechanisms to allow players to pull an NPC into a scene to shift the tone back. Investigation can really only happen when in the darker tone, which gives players a reason to shift it back (one player can shift out of dark mode, all players must agree to shift back in)