A couple things.
First, did he have a full security clearance or an interim clearance? The reason I ask is that, unless things have changed recently, there's a large backlog on background checks. They can easily take months to come through. It's fairly common for an interim clearance to be granted until the full check comes through, and an interim clearance can usually be granted by a security officer of a certain grade (I know the regimental-level G-2 can do it, not sure about smaller organizations S-2 officers). I suspect there's someone of the appropriate level at the location. Basically, unless there's reason to suspect something or there are active warrants out, there's not a lot of check on these interim clearances.
Second, just a comment to Nessie, are you against anyone ex-military owning a gun? Because everyone who is no longer in the military has been discharged. An honorable discharge is what you get after you serve out your contract time and leave, or if you retire, or whatever. Basically, if you get an honorable discharge, it's a paper stating that the government was happy with your service, and agrees you've fufilled your contractual duties. I suspect this is simply a misunderstanding on your part of what a discharge is...I don't really think you intended to slap every military veteran in the face there
Finally, did any place mention what level of clearance he had? There are multiple possible investigations. For a Secret clearance, typically it's a national agency check and credit check. They basically check your name against national databases to see if you've had any crimes recorded, and run your credit to see if you have bad credit or high debt. I also believe this only goes back about 7 years. For higher clearances there's more involved, including visits and interviews with people who know you. Generally, you have to provide a character reference to cover the entire time frame of the check (in other words, you have to provide contact info for people who knew you through the entire seven years for a Secret, and longer for a Top Secret. I think TS goes back to 13 years, but can go back even further for particularly sensitive positions (not all top secret clearances are created equal); a friend of mine who worked intel had one of his high school teachers interviewed).
I also hope Sabrina shows up; this is her specialty area, so she knows more than I do. I worked computers (and medical, and combat engineering), so I had to obtain a clearance, which is where most of my knowledge comes from. The secret clearance level I know about, cause that's what I had. A bit fuzzier on the TS though.
