@_sims_Yimi
Ooh, great question! And I can actually answer this one!
I started with an idea that just wouldn't die, so wrote a very brief plot outline. Then I went through the whole story in my head and wrote bullet points. Then wrote around each bullet point until I pretty much had a novel. Then I added page breaks where I thought chapters should be (these are prone to change), printed them all out and muddled them up, generally trying to make the story as tangled, complicated and frustrating to write and read as possible. ;)
Then I started playing the story. I haven't finished that part, yet. Sometimes, something will happen when I'm playing that I'll add in, and sometimes I get a random idea and throw that in, too. But generally, the writing is done. This is not a method I recommend, but is one I seem to be repeating for part 2. :D