Nathan Stone is an agent with the Commission.
Assassin is a better word for the work he does for this unofficial and definitely unauthorized organization. "The beauty of the Commission was that they didn't exist. Not officially. A back channel with the Pentagon ensured that only a select few were in the loop." If you asked any of the members of this group what the purpose for the Commission was, you would undoubtedly listen to a long spiel about preserving the nation and eliminating the enemies both inside and out that threaten it. In truth, it worked to keep the power of the government in the hands of those they wanted. Anyone who looked like they might challenge that power structure were put on the list of people needing removal.
Stone is one of those removers.
He did not plan on being one and was not happy to learn that he was slated for such a position. He might have put up a fuss about it sooner than he eventually would except ghosts don't have much of a say in their situations.
And Stone is a ghost.
This former delinquent from the tough streets of New York's Lower East Side found a way out of that neighborhood through the U.S. Army, more specifically Special Forces. The field reports coming from his actions in Iraq showed "fearless soldier". They also showed a man "reported ... for unlawful deaths and killings" in some cases. While this made his superiors more and more nervous, it attracted considerable interest by the CIA.
Transition to the Agency came quickly and so did the training at The Farm where he "learned to bug phones, use dead drops, read detailed maps, and put suspects under surveillance undetected". He also honed his killing skills with knowledge of poisons, untraceable drugs to bring about heart attacks, and use of other quick and lethal weapons like the garrote. Stone proved to be an excellent killer for the Agency. Until he died.
Not fully, of course, but officially.
That is when the Commission came to call.