During the U.S. invasion of Afghanistan more than eight years ago, the CIA officer worked closely with McChrystal, who was then a commander of elite military commandos. The CIA official is well known in CIA lore as the man who saved Hamid Karzai's life when the CIA led the effort to oust the Taliban from power in October 2001. Karzai is said to be greatly indebted to the CIA officer, and was pleased when the officer was named chief of station three years later.
In the end, however, the officials say, it was the CIA officer's long relationship with General McChrystal that was the deciding factor. Rather than find another candidate, the agency gave McChrystal's friend the job.
That McChrystal, an Army general, was able to install a friend as station chief, said a former official, was indicative of both McChrystal's pull and the reality of the Afghan war zone, where the military now has a greater presence than it did just a year ago. "McChrystal can have anyone he wants running the CIA station," said a former senior intelligence official who now consults for the Pentagon on Afghan issues.
Geoff Morrell, a Pentagon spokesman said, "As far as I know, just as the Defense Secretary picks his top commanders, the CIA Director picks his station chiefs."
According to two current and former intelligence officials, the official who was the agency's first choice told colleagues he was frustrated by the decision. Instead of going to Kabul, he kept his job as the chief official in the CIA's European operations division.
At the request of the CIA, ABC News is withholding the names of both the CIA's original choice for the job and the official who got the job because both are still undercover.
CIA spokesman George Little denied that Holbrooke or McChrystal had any involvement in the agency's decision.
"The CIA makes its own personnel decisions. Period. That's all there is to it." The intelligence officials, who requested anonymity when discussing sensitive personnel matters, have no problem with the officer who was eventually chosen by the agency. But they said the agency clearly preferred someone else, and they fear the CIA has become subordinate to the military, after many years dominating U.S .efforts in Afghanistan after the September 11th attacks.
"We were in the lead after the invasion, but clearly the CIA has taken more of a support role," said a former senior official who served in Afghanistan.
The current and former intelligence officials say that putting a paramilitary officer in charge on the Afghan base highlights the CIA's evolving role. The CIA's historic wartime role was collecting information in order to shape overall strategy. Now the agency has been relegated to a supporting role, supplying tactical intelligence to help the military. The military determines the strategy.
"The CIA is supposed to be a check on the military and their intelligence, not their hand maiden," said Robert Baer, a former CIA case officer. "This is a sign of things to come, where the military dominates intelligence."