OK, I came with the idea today - it's not very original, but I think no one did level like this before.
I am sure everyone of you played, or at least heard about Half Life - it's known mostly because of its atmosphere and plot - how about making a Half Life-style-level? Juni is a scientist, who take part in researches about unknown matter, which can be used as a power source. Finally, her team decided to make a risky experiment of merging high amount of this matter, to see if it's safe. It wasn't. When the experiment turned bad, all scientist left the complex, with Juni trapped inside. While she tries to escape lab, she finds out what was the real purpose of creating this matter, and why the complex is now abandoned.
Huge, custom map with lots of puzzles. Sounds good?