Okay, so you've got your idea and a bunch of interesting characters. What now?
Time to get plotting. (Cue mad scientist laugh.)
Without rehashing to the old pantser/plotter argument, I do feel it's good to have some loose idea of the plot before you start writing your story. Bare minimum? The ending. It might change as you write, it probably will, but at least you know what you're aiming for.
There is something to be said for a short outline, though: it's much easier to spot and fix plot holes at this stage. If you jot down the major twists and turns of the plot and then think about what the reader expects you to do, you can come up with something very unique and original instead. If the reader expects you to zig, maybe you should zag? It's a fine line, though. Do too much of this and you'll risk alienating the reader. Sometimes it's fine to do what's expected, especially if it's something that defines the genre. People reading a love story expect the characters to end up together. If they end up getting horribly killed by mutant zombie dinosaurs instead, your readers might get a bit miffed.
For a short story, side plots can add extra weight, but they can add depth as well. Does the side plot explore the story's theme from another point of view, or maybe mirror the main character's journey in a way? How will the side plot merge with the main plot at the end? For a cohesive story, the side plot should have a point to it in the context of this particular tale, not be separate from the main storyline. Figure out what's best for your story.
We'll talk about story structure and character arcs later, but for now, think about how your protagonist will change during the story. Is the change positive or negative? What will she learn? Or is it a flat arc story, as in the protagonist changes the world in some way instead of changing herself?
If you want an example of great plotting in the speculative fiction genre, check out any book from Jim Butcher's Dresden Files series. I guarantee you won't see the plot twists coming. Harry gets into all kinds of scrapes, but he never takes the most obvious way out, or often it's not an option, so he has to be more inventive, which makes for a very entertaining story.
Day 1: The Big Idea
Day 2: Cool Characters