[Yes, I know that this supplement has been adapted into a different and increasingly popular game with its own dedicated podcast - I don’t want to talk about that game in this topic, so please don’t bring it up, thanks.]
Graham Walmsley deeply understands what makes the original Lovecraft stories tick. In 2011 he published Stealing Cthulhu a book that extensively dissects Lovecraft’s stories and explains how to use what is found there in RPGs. In an appendix of the book he put his tiny set of rules for Cthulhu Dark. If we are to trust archive.org, Cthulhu Dark first appeared as a separate freely downloadable four page pdf circa September 2012 and its three page scenario writing guide Dark Depths followed a few months later in January of 2013. Cthulhu Dark would eventually go onto a Kickstarter in May/June of 2017 expanding the four page pamphlet to a 200 page book (print|pdf). For the most part everything in the original Cthulhu Dark pamphlet went into the book (though “Sanity” thankfully was replaced by “Insight”). Sadly the scenario design suggestions from Dark Depths were not ported, which is a shame, because to me they are absolutely fantastic and are a perfect easy to use distillation of some of the ideas from Stealing Cthulhu. (Or at the very least they do a fantastic job of helping you quickly create scenarios that feel like the original Lovecraft short stories. (Minus the racism, xenophobia, etc.))
(I’d recommend reading the pdf. It is all of 456 words… I’ll wait. (Oh, and yes, it should be 1,2,3,4,5 not 1,2,3,3,4))
So after you figure out what the creature causing the trouble is (he says Mythos creature - I think you can go that route (I’d recommend Stealing Cthulhu for examples - Graham goes through many of the main ones with how-to-integrate-them detail) or come up with your own) and figuring out where it is happening he recommends a five level onion-like structure for what happens through the scenario. Before moving onto occurrences from the next layer two occurrences from the current or previous layers must occur. (Though I would say if you wanted to extend the scenario’s length you could see two as a minimum.) So in layer one, two things from the layer one list must be encountered. In layer two, two things from either the layer one list (those not already encountered) or the layer two list must occur, etc. Additionally, there are some entries in each layer (and interestingly all four entries in layer one) that point towards or gesture towards things in deeper layers (even though those haven’t been fully unearthed yet). Finally there are environmental requirements for moving into layer two (the Investigators must be somewhere that is at least two of the following: malodorous, unsettling, decaying, remote) and for moving into layer five (the Investigators must be somewhere that is at least two of the following: dark, underground, ancient, alien).
What is so amazing about this setup and structure is that it gives the GM the ability to choose a kind of slider of explicitness and improvisation at both the prep stage and while at the table. If you prep say the minimum number of occurrences (so 10) and it turns out the players move through to layer three but don’t seem to be aimed at your next two occurrences - you can improvise some occurrences that would fit the current fiction based on the bullets in Dark Depths. That may end up making it hard to integrate the other occurrences you had planned, but you at least have all the pieces necessary to keep going. And the reality is your players will never know - because it will just feel like a Lovecraft story because of the things that occur and the locations where they occur.
This structure also reinforces the idea that progress should not halt due to “missing” a clue. The mechanics of Cthulhu Dark itself enforce this, but that this scenario design system echoes it as well just makes it even better in my mind. (And in reality it allows you to use whatever rules system you want.)
(Also, if you happen to get Stealing Cthulhu, read it in Adobe Acrobat Reader so you can see all eight different layers of “edits” by each of the “editors”.)