Write down your story's theme and plot theme. Organize your plot theme into specific conflicts to use in your story. Separate these conflicts into those that will become your primary story arc and those that you will use as subplots.
Separate your primary conflict into plot turns. These are occurrences in your story where your primary plot faces a significant challenge or is influenced by an outside force. These occurrences become sections of your story. Read these sections individually and plan how you will turn each section into a series of chapters.
Lay out your chapter plan and read it. Make sure that these chapters make sense and follow a cohesive pattern through your story. Insert your subplots into specific chapters where they function both to tell their own story but also to enhance your primary conflict.
Label your primary conflict as well as your subplots. Go through each chapter, labeling every instance where your plot and subplot show up in your story. Read each of these plots and subplots and ensure that each are complete stories with a specific beginning, middle and conclusion.
Write an extensive character study. Examine every character in your story against your primary theme and consider how they will approach this theme as well as how your theme will change them. Make specific notes about each character's personal traits and use these traits to reinforce your themes. Describe your character's psychology and history.
Read your chapter plan backwards. Make notes for each event in your story that requires a device. If a chapter requires that three of your characters show up in the same place, you will need to plan how to get them there in a prior chapter. If a character requires that a specific tool or instrument exist in a setting in one chapter, you will need to define how it is in this setting in a prior chapter. Close any plot holes that remain in your story.