I'm waiting a bit before forming a solid opinion on this NSA mess.

[MineralMan]

45. Typically, the organization in question makes the final decision.

Security clearance investigations are primarily done by the FBI, and for high-level security clearances, are quite thorough. For the highest level clearances, which include Top Secret and Top Secret with additional endorsements, that investigation will include criminal background checks, a thorough life history assessment, and personal interviews with people who know the person being investigated.

Today, a good deal of the investigation involves online investigation, but the footwork is still done, as well. When I got my security clearance in the USAF, at the tender age of 20, the FBI went to my little California home town and interviewed a couple dozen people, including teachers, clergy, employers, neighbors, and more. The application for that clearance was very detailed and involved a huge number of questions that required truthful answers. Each one of those questions was investigated. They even included details of mail I had received from foreign countries during my life, and all organizations I had ever belonged to. They checked each answer carefully.

In my case, for example, I had been an avid short-wave radio listener in my teens. In doing that, I had sent reception reports to many, many foreign radio stations so I'd receive the pretty QSL post cards acknowledging my reports. Some of the countries were Communist countries. Some of those also sent literature to me beyond those QSL cards, including subscriptions to propaganda magazines. During that time, all mail from the Soviet Union, China, and other communist countries was recorded and the recipients added to a list of people who received such mail. I disclosed that on the security clearance form and got questioned in detail by an FBI agent who visited me at the USAF base a week later. They also asked my parents to show them any such mail I had retained. Apparently, my explanation of why I had received such mail was satisfactory, since the clearance was granted and enhanced several times during my enlistment. But the investigation was very thorough.

That was the process in the mid 1960s. They didn't have online resources then. Now they do, but the process is, I understand, still similar. FBI field agents do a lot of the legwork, and then make recommendations. The issuing organization makes final decisions, but I doubt they would go against the FBI recommendations.