John Clark is an agent with the CIA.
Well, he is for quite a few years of his life. He had a life before then and he definitely had a life after his time with the Agency but when we first meet him he is an agent in very good standing. In those time after he was pushed out of the CIA it could be said 'he is an agent with Rainbow Six' or 'he is the Operations Director of The Campus' (more on them in a moment).
Born John Kelly in Indiana towards the end of the Second World War, he attended parochial school growing up and even went to a Jesuit Preparatory School before changing directions. That change took him into the Navy and into becoming a SEAL not long after that group came into existence. His service would take him to Vietnam where he would be involved in several deadly operations which would in turn result in his being highly decorated. A Silver Star, A Bronze Star, a Navy Cross, and three Purple Hearts, among other things would find their way into his record.
When his tour in Southeast Asia was over, Clark left the military but was soon approached by the CIA with an offer to be part of the Special Activities Division and a return to Vietnam to mount a POW rescue mission. Before he left for it, he wrapped up a personal war with drug dealers in Baltimore which had resulted in the death of a young woman close to him. Unfortunately since the police had evidence that it was Kelly (Clark) who was behind the deaths of several less-than-pleasant individuals and looking at a life behind bars, John Kelly 'died' and John Clark came to be. Having a major government bureau like the CIA take care of the details helped immensely.
During his life in the Intelligence community, Clark would work for the CIA and then, when an idea presented by Clark resulted in the creation of a NATO response team to be quickly deployed to handle terrorist activity, he would be the one to head one of the teams. After that when political winds start to change, Clark would be a major player in an off-the-books organization called The Campus.
Not bad for a dead man.