Board Thread:General Discussion/@comment-10941901-20130723221328/@comment-8245466-20130724191521

I've decided it's likely that the Patriots never bothered to control Foxhound, being that they already controlled the CIA, FBI, DOD, etc. Foxhound never operated on its own, so unwittingly Foxhound were always Cipher's dogs of war. Since Zero and Ocelot were interested in researching soldier genes and the results of the Perfect Soldier project, it's possible that Dr. Clark was made the chief medical expert of Foxhound in order to continue the Perfect Soldier project using Foxhound agents as test subjects for gene therapy using Null's DNA. This could be where Those Who Don't Exist come from, and provide a reason for Big Boss to retake command of the unit.