This is probably not something I should admit as a writer. Don't tell anyone, but plot is usually the last thing I think of when developing a story.
Combine that with my trouble with setting, and you have my two greatest weaknesses when it comes to writing. In both cases, I've discovered that the solution is simple in theory, and more difficult in practice: preparation.
For me, the general writing process can be broken into two parts: the easy part, and the hard part.
The Easy Part
This is the beginning. It's that flash when the idea comes in the middle of the night, the new character that walks into my head brandishing a sword and demanding to be put on the page immediately.
Sometimes, this phase only lasts a few paragraphs. Sometimes, it lasts most of the novel, like it did during the marathon that was the writing of the second Cassie Tanner novel (ten weeks, the fastest I've ever written anything longer than a school essay). During this portion I write quickly, passionately, using up every spare moment to get the ideas out before they get scared away by things like my day job or sleep.
The Hard Part
This is where the research and the planning take place. Once that initial burst of creative energy wears out, I turn away from the computer and usually go to either a notebook or the typewriter to work out the next phases (I've also been known to switch the fonts on my computer temporarily to something period or story appropriate. Currently, Olivia is being written in Pages' Kokonor, an italic serif font that borders on script).
Sometimes, I start with research, trying to find out more about the historical or geographic setting I've chosen (or that the characters have chosen, as the case might be). Other times, the problems lie in the actual construction of the story.
Somewhere on this blog, there is a photograph of a flow chart I created some time ago for Threadbare, back when it was still Fortuna Mulibris, or possibly even before. I can't find it now, and I usually throw out my notes once I've either written the sections they cover or made such drastic edits that the manuscript no longer bears any resemblance to the notes, so I don't have anything recent to show you.
Anyway, the flow chart is my basic form of plotting out the actions of a character. It's usually sketchy and brief, and takes up no more than two pages. It frequently does not reach the end of the manuscript and more of a stream of consciousness outline of what I would like to happen than an actual route for the story to follow.
More recently, I've begun using an outline. Just like you learned in school, I start with a chapter heading and move chronologically through the events that should happen in that chapter. I've been writing long enough that I usually have an idea of how long each of those scenes should be, and have an idea of where to put the chapter breaks in advance. In most cases, I'm pretty accurate. Sometimes though, the story decides to take a wild left turn and I end up being way off. But again, these are only guidelines.
As I'm working on the outline, sometimes I think of things that need to happen, and I'll add them in the margins. If the notation needs to go in a specific place, I simply draw an arrow from the note to the proper place in the timeline.
Once I have the timeline worked out, I can go back to the manuscript and continue following my bullet points to construct the story.
I have one more short blog planned on this subject to cover the miscellany I haven't talked about yet, but if there is something specific you would like to know, leave a comment and I'll try to work it in.