MARY LOUISE KELLY, HOST:

A few years back, I was interviewing a man who had held senior posts in the CIA's clandestine service. I asked him a question, and he scratched his head and said, let me look that up. Off his shelf, he pulled not a fat, classified file but a copy of "Ghost Wars," the book by journalist Steve Coll that chronicled the history of the CIA, Pakistan, Afghanistan and Osama bin Laden. It's like the Bible, the CIA veteran told me - closest thing we've got to a definitive public record of what happened.

"Ghost Wars" covered the period up to September 10, 2001. Coll's new book picks up the narrative from there. The title is "Directorate S: The C.I.A. And America's Secret Wars In Afghanistan And Pakistan, 2001-2016." When I spoke to Steve Coll, I started by asking him, what was the big question he set out to answer in this new book?

STEVE COLL: Well, how did we get from the 9/11 shock to the 17-year war and the stalemate we're in now? And particularly, how did three administrations now but primarily the Bush and Obama administrations in my history wrestle with the complexity of the war and fail to solve it?

KELLY: What you're saying speaks to one of the threads that runs through this book, which is how over the years the U.S. position on, say, the Taliban, who was - you know, the U.S. went in and started fighting them in 2001. And we still, 17 years later - on the one hand, the U.S. continues to fight them in Afghanistan. On the other hand, there's still an acknowledgment that this is not going to be won militarily and they need to come to the negotiating table. This question of, who are allies and who are enemies - they shift, and then they shift again.

COLL: Exactly, and so do our war aims. Are the Taliban our enemy? You know, they didn't participate in the 9/11 attacks. There were no Afghans on those planes. Of course they were complicit in a legal and moral sense because they harbored al-Qaida as al-Qaida planned the attacks. But, you know, it's not even clear the Taliban leadership knew about 9/11.

And administration after administration really struggled with the question of, do we the United States really want to fight a war against the Taliban? They're part of the fabric of Afghanistan. They have physical sanctuary in Pakistan. They can self-finance through the drug trade. This is not a war we're going to win. And yet this problem of whether the Taliban was really an enemy of the United States was never fully resolved.

KELLY: I mean, just to pause there, that's a stunning thing to say - this idea that in 2018, after 17 years of fighting, it's still a question who the enemy is. That's mind-blowing.

COLL: Yeah, I mean, today we're fighting two wars in Afghanistan because the enemies are different. And one is against the Islamic State, which we do identify as direct threats to the United States and our allies in Europe. And then the second war against the Afghan Taliban is an advise-and-assist war where we support the Afghan Security Forces in their civil war against the Taliban. And we basically function as their air force and their intelligence service.

But we don't really see a pathway to victory, and we just stay at it because we are committed to that constitutional government. And if we withdrew, it would almost certainly collapse, which would create even greater dangers.

KELLY: I want to get you to tell me a story. As a reporter covering national security, I interviewed a lot of the same people who turn up in your book, one of whom was Gary Schroen, the CIA officer who led the first team into Afghanistan right after 9/11. I flew out to Nevada where he was then living in 2005 and interviewed him. And he told me so many crazy stories.

There was (laughter) one I remember about - that he'd put in a supply request for a hundred pounds of Starbucks Mocha Java, and the CIA actually helicoptered it into the Panjshir Valley and (laughter) dropped it for them.

COLL: (Laughter).

KELLY: You got another crazy story about his time there, about - he was on the ground in Afghanistan. He got a call from CIA headquarters about a Predator that was about to fire off a Hellfire missile. Tell what happened.

COLL: Right. So it involves a colleague of his who was in the Panjshir Valley immediately after 9/11. And this colleague's name was Chris Wood. At the time he was wearing a big, bushy beard, and he was kind of an operations officer on the ground. And Gary Schroen and Chris Wood had identified what seemed to be an old German airstrip in the valley that would help them create more landing places for helicopters coming in with supplies.

And so every day, with this big, bushy beard, Chris Wood would go out to this airstrip with a bunch of Afghans with guns, his security detail, and he would oversee the construction project. Well, this Predator started to watch this bearded man with slightly blond hair, not exactly Afghan-looking with a bunch of bodyguards. And these CIA analysts apparently concluded that he might be Osama bin Laden. And so they were about to vaporize him when they called in Gary Schroen to say, are you aware there's a guy with a security detail, looks like he might be an Arab floating around there? And Schroen had to explain to them that that was...

KELLY: Not Osama bin Laden but one of their own...

COLL: Not Osama bin Laden, no.

KELLY: ...That they were about to take out with a Predator drone. I mean, it speaks to another theme that runs through this book, which is how often the U.S. seems to have been its own worst enemy.

COLL: Yeah, it really is a recurring theme. There's a secret review done toward the end of the Bush administration where the National Security Council staffer who leads it and writes it creates a bunch of slides for the president, says 10 wars. We have 10 different commands out there on the battlefield. And they were actually not only at cross purposes but very poorly coordinated.

There's this amazing scene where the Americans are negotiating for the first time with the Taliban's political representative, a guy named Tayyab Agha. And they're going to go to the first meeting with German help at a safe house outside of Munich. This was 2010. And the Germans say to the Americans, look; we've set this thing up. But Tayyab Agha's nervous that if he comes to the meeting, it's just going to be a snatch operation and he's going to be sent off to Guantanamo.

So then the National Security Council staff arranges for his transport from Qatar to Munich. And they're so nervous that there might be some kind of target list down in the CIA bureaucracy that they don't tell the CIA about the flight because they're afraid that if they pick it up, there might be, like, some automated response in which he gets snatched. One part of the U.S. government deceives another part of the U.S. government about what's really going on.

KELLY: Wow. One question that runs through these 700 pages is whether the service and deaths of thousands of Americans in the war in Afghanistan has been worthwhile. What answer did you arrive at?

COLL: Well, you know, when you go back through the decision-making, you know, you have to feel like the government decision-makers who were responsible for weighing the costs and benefits of sending Americans to war didn't do all they should have. Everybody was clear-eyed about al-Qaida. But the heart of the war, the war that many American men and women faced when they went out to Kandahar or Helmand - it wasn't a war against al-Qaida. It was a war against an indigenous, sometimes abhorrent but locally rooted militant group, the Taliban.

And the Taliban kept saying in these negotiations, you know, we didn't attack you on 9/11. You say we're responsible for 9/11 because we harbored al-Qaida. OK, we can disagree about that, but we have not fought you since then. We're only here trying to liberate our country from your presence. And the United States just could not come to terms with that basic problem with the war.

KELLY: So are you going to have to write a volume three of this? I assume you embarked on "Directorate S" with the hopes that (laughter) at some point the war would end and you could write a closing chapter.

COLL: I think I'll have to pass this role down to the next generation of journalists. But I do fear that there's no end in sight to the actual war on the ground at the moment. After all, even though the Trump administration is increasing the troop level a little bit and bombing a little bit more heavily, we've got maybe 15,000 maximum troops out there now. At the height of the Obama administration's surge, there were a hundred thousand Americans - you know, the best-trained infantry force in the world, and they couldn't change the war. So I don't see how this formula's going to do it.

KELLY: Steve Coll - his new book is called "Directorate S: The C.I.A. And America's Secret Wars In Afghanistan And Pakistan, 2001-2016." Tomorrow we'll have part two of our conversation - why Pakistan, our ally, would undermine U.S. efforts in Afghanistan. Transcript provided by NPR, Copyright NPR.