Before writing a word, take some time to jot down key story points. As you're writing, the story will want to take on a life of its own. Having a handy reference of key points will help keep your story on track and you from pulling your hair out. A list of key points is also helpful when outlining the story plot. You may very well find that the story begins to unfold as you're writing down the key points. If this happens...let it! Write down any ideas or details that come to you, they'll come in handy later.

Some key points to consider are; what is the mystery? This is the underlying theme to the entire story so be as in-depth as possible (has there been a murder or a theft or a kidnapping? If so, how and where was it committed?).
Hunt for the culprit. Every good story has at least one antagonist, but what steps must the hero or heroine take to find him/her? How will the villain evade the hero? How is the mystery solved? In mystery writing there are a lot of twists and turns. Write down your initial thoughts for plot twists, red herrings to throw the readers off the trail of the true villain, and of course the final stages of how the good guy will prevail...or does he? You need to decide whether or not the hero or the villain wins in the end. Many hero’s die trying to solve their case. Many are involved in physical altercations with other characters. You must decide how many altercations, the number of characters involved, and what weapons if any are used. It is not a good idea to only engage your characters with fist fighting. Throw in some knives, chains, falling from windows, or my favorite, a poisoning, and other nasty assaults.

Every great story has well rounded characters. We read fiction because we want to be entertained and develop a connection with the characters. Outlining items such as personality traits, physical features, and quirks can help bring your characters to life; a speech impediment, or limp, or a nervous twitch.

For the Protagonist, decide the name, age, where does he/she live, does he/she have a family or pets, what is their driving goal for taking on this particular case? Is the hero a police officer, a person sworn to honesty, pride, and valor. Or is the good guy a private detective being paid to find a certain someone. Or your main character could be a parent or sibling searching for a missing loved one.
For the Antagonist, decide the name, age, where does he/she live, is there an underlying reason for being the antagonist? Perhaps this person is a career criminal. On the other hand, maybe he/she is a good person that suffered an unjust and turned to crime out of bitterness and despair.
Then you have your support characters, who are the color of the story. They provide depth to the story whether good or bad. A support character could be as simple as a loud mouth hot dog vendor standing on a street corner or as in-depth as the villain's partner in crime. In writing a mystery story, support characters can take on a life of their own with the reader, so make them interesting. Just because they are labeled support characters does not mean they are any less important than the main characters.

Next is the location of the story. When and where is the story set? These two key elements are what bring your story to life. Mystery story writing is a broad genre and could be set in any time period and in any place. When working with actual locations it is a good idea to do research on the location first. Readers want to feel as though they are there with the characters, so being able to accurately describe a location is vital. Time periods are no exception. If the story is set in 1940's New Orleans, the reader will want to see their surroundings, not just be told the story is taking place in a speakeasy or church. Be descriptive!

A mystery story is not a story without a solid well thought out plot. Some things to consider when developing the story plot: What is the driving force of the mystery? To solve a murder, or rescue a kidnap victim? What does the villain do to thwart the hero? Does the villain get his goons on the hero? Is the hero being set up by the villain and now he is being hunted by police. What other obstacles get in the way of solving the mystery?

One of the most important elements of writing a mystery story is suspense. Giving away too much too soon will bore the reader. It is best if the suspense is sprinkled throughout the story; bring the mystery to light within the first few chapters, then as the story progresses add a clue here and there without revealing the outcome until the final chapter. Do not be afraid to add a "red herring" or false clue, within the stories context. Readers love nothing better than to think they have everything figured out only to find in the end they were mistaken the entire time.

The final few chapters of the story should hold the climax of the conflict and resolution between the hero and villain, including how all of the clues scattered throughout the story cumulatively solves the mystery. A good conclusion gives the reader a sense of closure in finding out how the hero solved the mystery. Remember that not all mysteries have to be completely solved or have a "happy" ending. If you are writing a series of stories, the villain may get away at the end of story #1 with the hero using clues from story #1 to track down the villain in story #2. In mystery story writing, the possibilities are only limited by your imagination.