Plot is the structure you impose on the events in your story. You select which to include, in what order, and how to tell each one. You shape your plot from raw material - the story.
You could start with the discovery of the murder, continue through to the killer's apprehension, explain in flashback or dialogue what went on in steps one and two:
You could start with the actual murder, masking the identity of the killer.
The steps may be ordered any which way depending on what kind of book you want to write.
Starting out, you could have in mind a beginning situation, a few characters, a background, a theme, and a hazy idea of the ending. You can start a novel with a minimal idea of where you're going, develop some ideas and characters, experiment with them, keep what fits, discard what doesn't.
Don't forget to bring conflict into your story. Let the supporting characters grow, come to life. Some of them may become more important to the story than you first thought. They could bring into the story conflict that will help develop your plot, or further complicate the plot.
At this point - the end of your primary development stage - you can take full advantage of free-form plotting. You have your characters in all their individuality and richness; you have a situation that is ripe for additional complication; you have an idea of where you're going. Now is the time to find out exactly where that is - and how you're going to get there.
Now, ask "what if" questions to developments that come along that your not sure of to see where you're going. You may find yourself in the middle of a new plot twist.
Free-form plotting requires constant readjustments of scenes and details to make them consistent with one another.