Company sponsors Secret Clearance just like H1B. This clearance is only for US Citizens for working in classified projects under DOD. You need to have clean records on your all activities including your foreign relationship. You need to surrender foreign passport during the process of Clearance. Clearance level goes in various levels such as:
Secret Clearance, Top Secret, SCI, Poly and so on...

I do have Active Secret Clearance. By the way, my group is looking for a US citizen. Are you looking for one in software development?