I had a Top Secret codeword clearance which required an extensive investigation by the FBI and was then granted. When I went home on leave, my friends asked a whole lot of questions but by then I knew to just keep my mouth shut. I was a sailor.
I had the same process. The Navy started the clearance process and the FBI did the investigations. After I was vetted by the FBI, my top secret clearance was granted by the Navy/DoD.