Jonathan West is an agent with the CIA.
More specifically, he is an assassin. He would be the first to point out the distinction so it seems reasonable to take the man at his word since lying about being an assassin seems a lot less common than being one and saying you weren't.
He is also an MD and he is quite proud, understandably, about that achievement as well although again he would willingly admit to there being a bit of a conflict between his licensed medical profession and the Agency's orders to terminate with extreme prejudice various people.
The very opening paragraph of the first recorded adventure gives a pretty interesting explanation of sorts: "My name is Jonathan West, MD-collegiate hockey all-American, Ivy League-educated physician, adjunct professor of medicine, pharmaceutical industry executive, US government assassin (retired). If you Google me, you'll find several pages of material written either about me or by me. It's all relatively benign, the chronicle of a successful physician in the pharmaceutical industry, interesting to only a few. You'll not find any mention of my government work. If you review the newspaper headlines of the seventies, eighties, and nineties, you'll read accounts of death and mayhem, large and small, that altered the course of this country's policy or history. Some of it was my doing, but the accounts are without reference to me; many of these incidents are presumed to have been accidents."
He then explains, sort of, that "I wasn't always an assassin; I grew into the job". Further, "I didn't wake up one morning and decide to be an assassin. It wasn't a career choice! It was a series of small steps".
West always wanted to be a doctor and was on his way to achieving that when his interest in hockey and a hope that maybe a career on the ice might also be possible caused him to take a break between his undergraduate years and moving on to med school, all to see if he would be called up by the NHL. He wasn't. He was, however, called up by the army and seeing as this was the late 60s, Vietnam seemed a reasonable destination.
Except it wasn't and he ended up in a sub-branch of Military Intelligence and stationed at the Pentagon. It was there that one of the many items of discussion was the matter of hijacking a plane for profit and West, after a few drinks at the local watering hole, came up with an idea that somehow made it to higher-ups and ... eventually West would be asked to enact his crazy idea and that is how he went down in history as a chap dubbed D.B. Cooper.
After that, the CIA and a career in assassination alongside Harvard medical school and a career as a doctor.