Outline your story in advance and make notes about all facts you need to verify, interviews you need to obtain and affidavits you will need signed. You can write about facts and matters of public record in your true story without fear of libel, but you'll need to set time aside to verify that the things you're writing about do fall into one of these categories.
Consult a lawyer upon completion of your outline. Let your lawyer take a look at the story you want to do and take his advice on the issues you will need to address before you begin writing. Your lawyer can give you advice as to what you can and cannot write. The laws regarding ownership are sketchy in the area of owning the rights to a story that hasn't been written. Technically, you can write about something that has happened to someone else so long as you aren't mentioning real names, but the safe bet is to contact the main party or parties involved and bring them into the project, either as consultants or by paying for the right to tell their story. A contractual agreement is always one of the best defenses against a libel suit.
Obtain a legal release from anyone you need to include in your story whose name or actions are readily identifiable to the public, especially if the role they will play in the telling of your true story is a matter of opinion and not a matter of public record. Hearsay or getting a story perspective from limited perspectives can lead to misrepresentation of the facts and set you up for libel.
Record interviews with anyone you talk to regarding the story, sign contracts and affidavits in the presence of your attorney and keep records of any research you do during the course of writing your story. Should a libel suit ever arise, all of this will be helpful to you in front of a judge.
Include notice in your work that you have taken all steps to ensure that every aspect of your story is true and that any misrepresentation was unintentional. This is no guarantee you will be protected from a lawsuit, but it does serve notice that you are basing your work on verifiable facts.