Personally, I start with the core of the story. Everything else (structure, aesthetics, style, etc...) has to revolve around it. If I don't have anything solid and truthful to convey, then I don't have a story.
Once I have that, I try and build the plot and the characters to convey and express it. Sometimes I get an idea or a situation or character first, and then I try to find the core of the story, see what I could convey through those situations and ideas. Basically, I write the story from the inside out, that way I don't waste my time on aesthetics or symbolism or anything that is just surface deep and will eventually come up anyways.
So I find a plot, an outline to follow for the moment, aware it'll need a rewrite, but it's a first step towards completion. Next is the backstory, which is simply what happens before the real story starts; and it doesn't necessarily have to written into the story. Usually the first plots and situations I write end up being used as the backstory or a secondary character's storyline or background. I save almost anything I write for this reason. I also find the plot to be the hardest to come up with and develop. A character's development is basically choices he/she has to make throughout the story, whether they involve action or just words; how he/she reacts to certain situations and obstacles is what makes him/her, and at the same time make the plot. It's that simple.
So I have a definite plot (or so I think), backstory, and research, which is what you should do when your blocked (Can't write anything? Do the technical and mechanical: Research). No characters' profile for me. It's just not my thing. I write their backstory, like a profile and their past in a small plot, all the way to where the story really starts. Sometimes the backstory helps you when writing a character in the subtle and inner ways. The character's backstory may not be written in at all, but it may still weight on her/his motivations and reactions.
Once it seems ready I try a more detailed outline. Basically, scenes described briefly, no dialogue. At this stage the aesthetics and symbolism start to come up, sometimes I'm aware of them, most of the times not.
I finish the outline, knowing it's going to need a rewrite, maybe lots of it. But there are always twists and points that stand out, and they begin to shape the story. I do all this having in mind the theme and core of the story. Anything that doesn't fit or helps, I just discard it. Also, have in mind you'll need a "counteridea", the opposition to the theme of your story. It may be in the form of a villain, or the inner contradictions of your lead character. You decide.
So I'm done with the outlining. Next, I try to line the scenes in a way to convey the meaning of the story- whether linear, non-linear, or just an antiplot. I also try to identify the symbols in it, the poetics and aesthetics, the inner contradictions of the characters and the inner symbolism.
All of this probably sound didactic and so self-conscious, but there's nothing wrong in knowing how something works. If you know the mechanics and how to make your story work, you'll get to something more complete and meaningful.
So I have a definite outline to start writing from, done the required research, everything but dialogue (only bits of it). I'm ready to write. The next is the most complicated and tiring step. This is usually when the self-doubts kick in, when the story seems to break apart and everything I've written begins to see as a waste of time. The times I've given up, this is the stage when I've done it. I rewrite and rewrite, pray and pray some more, until I get a first draft, which at the time seems like a miracle. After doing so much preparation and outlining it would seem the story will just flow easily without any problems- well, for me it doesn't. It just doean't seem good enough. So I go back- outlining, plotting, re-plotting, changing characters, etc,etc, etc...and re-write some more. This is basically how it goes for months, until I either try something else or stick it out until it comes to life. My main struggle is with the things I write about. I write about things I've seen and done and how I convey them, characters struggling with sins and the past, and some of those sins are disgusting at best. It's a real challenge to not only huminize a pedophile or a cold-blooded murderer, but to tell that God's salvation is offered and extended to them too if they repent is a bit harder. Because you don't want to victimize the characters, neither make them likable or justify their actions; you have to convey the fact that if they truly repent God will have mercy and save them- without sentimentalism or being overwrought. It's a real thin line you'll walk. And sometimes people choose not to repent, too.
Right now I have 3 stories in different stages, all of them which I once discarded and threw away. I couldn't get those ideas out of my head so I tried them and tried them until I got something different and original and truthful. One is a drama/sci-fi about disappointment and regrets and wasting one's life, which is the one I'm trying to finish up. I write screenplays, by the way.
And the most important thing to do before any writing: PRAY. You don't want to waste your time writing something that's not going to be useful or edifying to others. Tell God to give you the ideas. Do not come up with your and then tell Him to bless them. It doesn't work that way.