Zac Miller is an analyst for the CIA.
Jake Keller is a field operative for the CIA.
Put like that, it would seem two men are involved in this series but there is just the one.
When we first meet this gentleman, he is Zac Miller, a "strategic weapons analyst" and is considered one of the best at what he does but he is decidedly not a field agent. When in the first recorded adventure he volunteers to take the place of a blown agent on what Miller believes to be a very important op, he goes in knowing he is not trained and therefore not really ready but he believes he has a good chance of pulling it off. It goes very wrong.
So wrong, in fact, that when it all ends, it is necessary for Miller to disappear and so Zac Miller becomes Jake Keller. And Jake Keller has proven that he can survive really, really harsh conditions and come out on top and the CIA does not like missing such an opportunity.
And in that lies the problem for Miller/Keller. As his "handler" comments to him at the time of his "transition" from one person to another, "You had no language skills, no survival training, no money, and no backup plan, yet you successfully completed the mission after being arrested." He would add, "You have gifts that no amount of training can teach. There are people like you who risk their lives every day to keep this country safe. You know firsthand how ruthless our enemies can be. The field is your true calling. Zac Miller died in that van yesterday for a reason. Your new life in operations starts today."
On the one hand that sound like a good thing in that the CIA was providing a whole new identity to the newly created Jake Keller. The CIA was also holding onto all the proof needed to show that Jake Keller was really Zac Miller. Having something as powerful and, many would say, heartless as the Agency have that kind of power is never a good thing.