So they'd have blackmail material to use against potential leakers or defectors. They certainly did in the Edward Snowden case (remember the whole "girl is a stripper" thing that was meant to damage him but backfired?).
These are investigations for clearances. They ensure that the candidate doesn't have anything that can be exploited by a foreign government. The article mentioned this. Before you get a clearance you'll have to go through a very thorough background check. In the case of top secret information they'll dig into your entire life and even give you what's called a "full lifestyle polygraph", meaning no topic is off limits.
I was more answering their second question: "Why is it being stored?"
You've got to really want a job to go through that bullshit.