Read Call of Cthulhu 7e (And generally Lovecraftian horror) ! The part about how to run the game explain a lot on how to structure the scenario, how to create a sense of horror !
My advice :
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Start from the end => how do you get to the end of the mistery ? Have a set of clues, handout you cam give to your player when they are investigating that allows them to reconstruct the full picture !
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Hurt the characters personally => the cult of your RPG should try to scare away the character by hurting their loved one, they should be made dangerous to the player by directly hurting them! Show how unpredictable and dangerous this situation is :)
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Lock down access to information => they need to learn about witchcraft ? They'll have to steal books, travel around dungeons and be the first to get the resources they need to counter the plan of the cult.
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EDIT: Show the effects of the action of the cult on the world around the characters => unspeakable experimentations on the people of the city, and murders, property trespassed etc... This could be a hook!
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(EDIT: About the hook) The party could be asked to help... I don't know... The Magic Academy (lol) to recover a dangerous tome of forbidden knowledge and this could be what lead them down the rabbit hole!
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EDIT: TL;DR This should feel like a rabbit hole while you know exactly where they're going because you have lists of events, clues, riddles that allow them to get the big picture! Good luck with your project !
Use music made for Call of Ctulhu for ambiance !
Oh wow I wasn't old enough to witness the release the 6ed but I need to check it out to see the evolution of the rules