Yep sounds like the same process my mate is going through. He's been offered a position but in order to begin the role he needs a security clearance which is given by the national security, a different body entirely to his actual employer. It's pretty much the highest form of clearance you can get and you need it if you're going to have access to sensitive and secret information. He's even been advised to think twice about who he tells about the job, proper spy shit.
Plenty of people are rejected and they don't need to give a reason why which sucks. He's handed in his notice as well so could quite realistically be out of a job if today isn't a success.