I think its really an individual thing, everyone has a their own way of reaching a goal.
Me personally i always have a clear image on what i want to make in terms of a level, however i lack the skill to transfer that image to anywhere so it just has to stay in my head and a level usually comes out completely different than what i wanted it to look like.
If you want to make a series of some sort, i guess a good starting point would be time and place, make the levels represent that. If you want to be adventurous and don't lack imagination just keep making the story as you move on with the project and let it play out.
Usually when i get an idea of a story i easily recognize that its based on something i saw, read, heard. Don't be afraid to base your story off something that exists, usually it turns out that something like that has been done already in some form.
Making up something unique now is pretty hard, and what i see usually is people get frustrated and quit, don't do it, even if you are ripping someone its still a unique twist since you are adding your own ideas to the mix even if you can't see it at first, look at all the de_dust ports tell me it wasn't your first texture set when you made your first map for cs.
The basis for all my ideas usually comes from looking at images on Deviantart or a random search on google, but reading a book or something is also a great way to get that imagination flowing
Not sure if making any sense, but yeah here goes my 2 cents