I'm writing a story where the protagonist lives in a town that is thought to be abandoned, even though there is secretly an entire city beneath the radar. How do I write this? The last thing I want is to have it be a stereotype.
Start with your story's POV. Since your plot has a big secret hidden inside, you will want to tell it from a limited, non-omniscient perspective. It is that point of view character which is going to make your story unique. Who they are, how they see the world and what leads them to uncover the secret is what makes your story interesting.
Your story shouldn't be about a not-so-abandoned town. Instead, it should share a few days or weeks in the life of a special person and their one-of-a-kind point of view.
There's no intrinsic reason using a familiar setting means creating a derivative work. How many different stories have been set in New York, for example, or Paris?
If your plot and characters are original and distinctive, it shouldn't be a big problem if the setting is vaguely familiar --unless you're actually ripping off details from someone else.
What you definitely want to stay away from is having plot, setting and characters all seem suspiciously familiar at once (although even that can work if you're good enough --nearly all Shakespeare's canon was composed of adaptations of earlier works). A trick that has sometimes worked well for other writers is to place the plot and characters of one story in the setting of another --Star Wars is a fairy tale in space, for example.