Since the inception of the hobby, the dungeon has been roughly the closest thing any GM's ever had to a "script." The GM has this map, the GM knows where the party is on this map, the GM tells the party where they can go from the room they're in, the party chooses a direction, the GM checks the notes for the map to see what's waiting for them in the room they moved into, and so on. It's very straight-forward and intuitive. I daresay it's where a lot of the so-called "OSR movement" gets their strength; the dungeon is a time-honored, effective tradition for adventure creation.
That's all well and good for a hack-and-slash dungeon adventure, but what about a murder mystery? How can a GM prepare that?
Simple: make a dungeon. Or, as I call them, a mystery map.
A Mystery Map is the exact same thing as a dungeon, except instead of being rooms, monsters, and treasure, it's scenes, witnesses, and clues. I'm not the first person to come up with this, but here's my interpretation of it. Here's one I did up real quick to use as an example:
In this sample adventure, the PCs are looking into someone...we'll call him Mr. Victim...who's been mauled to death by a pack of wolves in rural Michigan. This seems highly unusual; not completely bizarre, as there's a death or two every season, but this particular mauling was along a relatively well-used hiking trail and it's very unusual to have an entire pack of wolves maul someone that close to civilization. Furthermore, the Michigan Department of Natural Resources (DNR) have tagged hundreds of wolves in the area and are usually very good at keeping the population to a manageable level.
The map starts at the bottom. That "S" in the box stands for "Start," as in, the first scene of the mystery. What exactly that is would be customized for the PC group; if they're cops, maybe they're in a briefing room; if they're private detectives, maybe a member of the victim's family goes to their office to hire them, etc. In the start "room," the PCs learn the nature of the mystery: in this case, they learn some dude got mauled by a pack of wolves in the woods.
The lines connecting to other boxes are leads, or clues, if you will. Here, I have three lines connecting to three other boxes. The line to the left leads to a scene involving the DNR, if the PCs decide to check with them about the unusual wolf activity. You see no other lines connect to that box; this means this "room" is a dead-end. The players may get some nice supplementary info, or maybe a chance to do some role-playing, but they'll find nothing directly at the DNR scene that will move the plot forward. The line to the right is a lead the PCs follow if they decide to do some digging on the victim himself. The line in the middle (which I forgot to write any notes on!) is if the players decide to directly visit the crime scene, which according to TV is the place that most detectives start their investigations. (on a revision, I may even consider starting the adventure at the crime scene, Law & Order style, since it's such an obvious move).
From that "room" on the bottom right, the players will, among other things, discover an important clue that moves the mystery forward: Mr. Victim is a convicted drug dealer. This will pique the PC's curiosity and have them thinking that perhaps Mr. Victim is not a victim of circumstance, but possibly to a drug deal gone bad? So perhaps searching his home will yield some more clues.
Notice that, unlike a literal dungeon, the players don't of course have to backtrack through the Mystery Map to get somewhere else. After discovering the clue about Mr. Victim's past, they don't have to go back to the first scene of the adventure before they can move forward. However, this can give a GM an idea on pacing and time. If the players have to "backtrack" through several previous scenes, then perhaps several hours or even days pass before the players can get to where they're headed. This can be a logistical issue (perhaps Mr. Victim lives hundreds of miles away?) or just a queue for the GM to throw out some random encounters (a sideplot, some complication of a PCs past crops up, etc.). A GM doesn't have to, of course; that's just an option, a way to "read the script," if you will.
Also notice that the crime scene has only one lead, directly to Mr. Victim's house. Off the top of my head, that means that the PCs will find some evidence the police did not...some meth hidden in a tree stump, perhaps. This sends the PCs to the same scene, but it now introduced a scene in between.
I think you get the idea, so I'll just gloss over the rest of the map; from Mr. Victim's house, we find two more leads; the name of one of his customers (we'll call her Ms. Wolf), and the name of his supplier (we'll call him Mr. Herring). Following Mr. Herring brings you to a scene at the casino where he works; there, the PCs discover the location of Mr. Herring's lab where his meth is produced. Going there reveals that the lab has burned down, written off as a meth explosion by the police, who still haven't figured out the connection between Mr. Victim and this lab. The PCs, with their clues, are able to put together (either from investigating the lab itself, or by pursuing Ms. Wolf) that Ms. Wolf was in fact the reason behind the explosion. Pursuing her (literally, perhaps, with a chase scene) brings us to "F", the Final scene: Ms. Wolf is a werewolf, and she and her pack are waging a vigilante war against the drug trade in the region. The adventure ends with a cliffhanger decision: now that the PCs know a pack of werewolves are fighting drug dealers in the region, what are they going to do about it? I'd listen to the discussion and prepare the next Mystery Map off of what I think they will do next.
So there you have it. As you can see, I pulled a lot of this right out of my ass as I was writing this post. Having the structure of the Mystery Map allows me to do this. I can see the key scenes of the adventure, see where I need to place those core clues to get the group from scene A to scene B, and I can also see places where I can stick in secondary/bonus scenes that enrich, endanger, or perplex the group.