I completely agree with Burger.
I know its fun to get into the engine and start placing entities and making a working level to run around in. We have all done it, but, this doesn't constitute a good game.
You must take the time to first, create the basic premise of the game and the general idea of what its about.
Start with the protagonist.
What's his/her back story?
What are they trying to achieve?
Where are they?
Why are they there?
Then move on to other characters involved.
What's their back story?
Why are they there?
What part do they play in the story?
Are they there to help the player or hinder them?
Next would be working out the players journey.
Do you want your game to be a basic run and shoot?
or do you want it to have puzzles and interactivity throughout?
Linear or non linear? Can the player decide which route they take?
Then work on the finer points of the story - the parts that might not be crucial, but, will add immersion for the player.
Try adding some side missions and collectable items. Maybe go back to the days of early Doom and give the player secret passages to discover.
These are obviously some very basic pointers to try to guide you to creating a story.
I am working on my new game Touch of Fear - Extinction. I already have the story in place, but, i am still adding bits to it and thinking of new ways to keep the player interested. I haven't actually fired up FPSC to start level design yet! I have been working on this game for a few months now (admittedly, I am eeking the story out a lot, but, i want to take this new game commercial, so, I am trying to make it the best I can)
If you have a crappy story, gameplay will be crappy, the player won't feel like they are part of the game and will lose interest.
Hope this helps.
Jay.
EDIT - On a side note, if you can learn how to make custom models, textures, scripts, sounds etc, your game will feel a lot more original. Don't just fill a room with generic models from various model packs. Think about your entity placement. Before you place each entity, really think about why you are placing it there! Does it belong there? can the player interact with it? what is the purpose for it being there?