A while ago, I did a little rant about my own personal caveats on writing mysteries. I'm not entirely sure how clear I was that these were only my personal methods that I have gleaned through investigation and research into the subject in my own way. What I said were more like guidelines than strict rules and one of the rules in my "Don't" section does have an exception that requires a little expanding upon.
When I said that using magic or the supernatural in a mystery is cheating, I only meant that in the context of it being used as a deus ex machina, but forgot to mention that it's perfectly fine to include it if you know how to implement it effectively and creatively instead of relying on it as a crutch to hand-wave away plot-holes and inconsistencies.
The best way to do this is to establish the rules, this doesn't mean you should spend pages just giving narrative exposition about the intricacies of the paranormal world you're choosing to weave into your mystery, but more just using the rules themselves as plot devices in their own right. This will allow you to weave them into the narrative and let you give a clear idea of what these phenomena are and are not capable of and how they work.
This is a mark of good writing and it's not actually as hard as it sounds, all you need to do is be clever about how you go about it. This process also goes for science-fiction where magic and ghosts can be replaced by technology and science.
The thing that will make a plot device like a magic spell, the existence of ghosts or your type II facial morphogenetic pharmaceutical injection system is establishing limits. Anything is possible in fiction, that's one of the greatest things about it, but sometimes anything doesn't mean EVERYTHING, if you've got something fantastical in your story it's going to need some ground-rules and the most important ones are not what they can do, but what they can't.
Let's say that one character happens to have a holographic mask that allows her to look like another person, these items are illegal for obvious reasons and so immediately you've got your first limitation: it's a black-market affair. With this simple fact laid out you've suddenly got so many possibilities to choose from for leads and plot devices: it's very rare, the software it's based on was a cheap hack-job and the underlying architecture is still present, the battery life isn't very good so it only lasts a few hours, the image quality flickers sometimes, the render was from an old photo so a scar or tattoo is missing and whatever else you like.
These will be great things for writing your story because they'll give you little things you can work from, I'll go over the list again and demonstrate little examples of how I would utilize information like that:
It's very rare: It's an illegal hack-job on a widely available consumer product, so firstly you should establish what the original product did and weave that into the narrative as well, just have a few people using it, maybe your main character finds it stupid or weird or maybe even wishes s/he could afford it themselves. Let's say it's a form of holographic make-up for people who just don't have time to make themselves look presentable (business people come to mind as an ideal market), this establishes it in your world, gives your world a little bit of character and shows how shallow and reliant on technology people can get, but, more importantly it's a soft-introduction to what you're going to be using it for later. The face mask is hacked and makes a prostitute able to look like whoever her clients want her to be for that night, all she needs is the right body type, the software will fix her face to look like a pop singer or some twisted fuck's little sister. So, you track down where she might have got it, who would be able to hack it in this particular manner and you've got yourself a bunch of plot and a bunch of leads.
The software it's based on was a cheap hack-job and the underlying architecture is still present: Your investigator doesn't really know where to find this hacker, so they've had an expert take a look at it, they were able to tell them that it's messy and the guy/girl who did it left some of the functions intact, one of them might be recording software or an in-built camera so that the holographic make-up device could instantly copy a make-up style while the user was walking around town. It's a grainy photo and it's not got the hacker's face in it, but there's some background stuff that your street savvy investigator recognises and that's their lead to finding the hacker.
Another thing that might be of note about the hacking job being sub-par is they disabled the animation software to boost the image quality, so the face looks incredibly realistic with barely any artifact hazing, but there's no emotion tracking software anywhere to be found so it can only manage minor blinking and mouth movements. This can be important because it means that the murder looked cold and emotionless when they shot/stabbed/poisoned an important political official during a big charity dinner because at first it would seem psychological, the killer is just cold and emotionless, but if the holographic mask doesn't react to emotions, maybe they were incredibly emotional at the time and the mask didn't have the capacity to show it. This distinction can have a great impact on your plot as maybe it switches the focus to another suspect instead of the one who seemed so cold and emotionless (with a good reason to be, I mean, come on, write a good reason for this guy to not be able to emote clearly).
The battery life isn't very good so it only lasts a few hours:
This is fine if you're a hooker, you don't need it to work for longer than a few hours, you want to get through as many clients as possible and forget the day even happened with a few shots of future drugs in your eyeballs. If you're a murderer using this as a disguise to murder someone, though, this suddenly becomes a problem. What if they assassinated someone important during a speech? They'll have to plan a lot of things around the fact that they don't have a lot of time to pull it off before the power gets too low for the hologram to remain stable. They'd have to make their escape quickly so you'd be looking for escape routes which would allow for this, which might include a quick costume change to become a waiter or just another guest at the hotel who could pretend they had nothing to do with the murder.
The render was from an old photo so a scar or tattoo is missing:
This is more a first lead, something that's noticed by your investigator to kick off their search, not something that comes in late game like the ones I gave responses for above. Your investigator notices that there's something missing and they look into it, they find out about the hack-job on the holographic make-up device and they follow that up further to get Mr Emotionless out of the frame and put a more likely suspect in his place.
As you can see, it's all just common sense and logic, but really establishing these ground rules beforehand for anything you plan in implementing into you mysteries that doesn't have a current grounding in reality should have verisimilitude; basic, logical rules that keep it grounded enough to be believable and prevent it from being overused as a catch-all cover-up of your own laziness. There's plot devices and there's just saying "a ghost did it". There's plenty of fun in being creative with this kind of thing, but you really need to look at it in a way that adds to the story in a meaningful way, not just use it as a means to an end.
Until next time, space pigs!