It's not easy to create an original custom story. I know, you have your story now, but here just an advice:
At first, you should think of the main aspects of your story. Let's just say it's about a man who is a
prisoner, and wants to escape. (Just an example). Now you have your main setting.
To build up a storyline, you have to note, what elements you want to bring into your custom story.
Like: A lot of monsters spawning? Shocking parts? Or just a creepy atmosphere, with evil mind traps?
-> Combine these ideas with your story. It should all work together, like a cog fits to the other one.
Finally, but more optional (but I think it's a good idea), add an optional story, which will be told
simultaneously with your main plot. This prevents that your story gets boring and dull.
This shouldn't take over the main plot! (but it can influence it, and maybe be an important part for the main story)
But like I've said, it's optional.
Now create your level design :3 (While designing the level, you get new ideas. Add them!)
These are my steps to create a nice storyline