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RACHEL MARTIN, host: From NPR News, it's WEEKENDS on ALL THINGS CONSIDERED. Guy Raz is away. I'm Rachel Martin. Admiral Mike Mullen retired this past week, leaving his job as the president's top military adviser. Mullen spent his four years as chairman of the Joint Chiefs of Staff trying to improve relations between the U.S. and Pakistan, which he sees as crucial to success in Afghanistan. In his parting remarks, he had some advice for his successor, General Martin Dempsey.

Admiral MIKE MULLEN: I urge Marty to remember the importance of Pakistan to all of this, to try and do a better job than I did with that vexing and yet vital relationship. I continue to believe that there is no solution in the region without Pakistan and no stable future in the region without a partnership.

MARTIN: Admiral Mullen was by most accounts Pakistan's best friend in the U.S. government, so admitting he wasn't able to keep that relationship from unraveling is a sign things have gone from bad to worse. And that's our cover story today. A lot of the tension between the two countries is over Pakistan's intelligence service, the ISI. That spy agency is at the center of a recent piece by reporter Dexter Filkins in The New Yorker about a Pakistani journalist named Syed Saleem Shahzad.

DEXTER FILKINS: Well, it's just, God, what a strange story.

MARTIN: Back in May, Filkins went to a coffee shop in Islamabad.

I met Saleem - I just met him in a Gloria Jeans coffee shop, and we were just chatting about a number of things.

Just that week, Osama bin Laden had been killed and Saleem was the kind of contact an American reporter could depend on for inside information about what happened. Saleem was known for his reporting on the ISI. Some suspected the agency of harboring bin Laden, and he told Dexter the ISI was watching him.

FILKINS: He wrote a story last year. Now, you know, this is when Osama was still alive, but it was something about how Osama was kind of on the move again, and he was meeting people, and he was crossing a border in Afghanistan that other intelligence agencies knew about it, et cetera, et cetera. This is back in March. And so he gets the phone call, you know, from the ISI.

MARTIN: And this sort of thing?

They said, get your butt in here.

The intelligence service summoning journalists? Not all that uncommon in Pakistan.

FILKINS: So he shows up at the ISI headquarters. He sits down with the generals and the admirals and they say, we didn't like your story last week. Saleem: Why is that? Well, we want the world to believe that Osama is dead, and you're making that harder.

(SOUNDBITE OF MUSIC)

FILKINS: Now, think about that. This was in March. This is when Osama bin Laden was still alive. Why on Earth is the Pakistani intelligence service saying to a reporter, we want the world to believe Osama is dead?

(SOUNDBITE OF MUSIC)

MARTIN: And this is the crux of what's so complicated about the U.S. relationship with Pakistan, the idea that the intelligence agency of a country that's supposed to be America's ally could actually be working with extremist networks. That is exactly what Admiral Mike Mullen said to Congress a couple weeks ago, that the Haqqani network, blamed for attacks on U.S. forces in Afghanistan, is working as a, quote, "veritable arm" of the ISI.

In choosing to use violent extremism as an instrument of policy, the government of Pakistan, and most especially the Pakistani army and ISI, jeopardizes not only the prospect of our strategic partnership but Pakistan's opportunity to be a respected nation with legitimate regional influence.

And that brings us back to the Pakistani journalist Saleem Shazhad. He never wrote about what the ISI had said to him about Osama bin Laden, but sitting in that Islamabad coffee shop, he opened up to Dexter Filkins.

FILKINS: I wanted to talk to him about bin Laden and about, you know, Pakistan and the whole thing, and he kept changing the subject. You know, he kept coming back to, I got to get out of here. You know, I got to get out of here. He kept saying that. I got to get my family out of here. And, you know, this was - I met a very nervous man. I mean, I met a guy who was afraid for his life.

MARTIN: About a week after that conversation, Saleem wrote one more article, this one about possible links between al-Qaida and the Pakistani Navy.

FILKINS: He disappeared, I think, you know, within a day and a half, two days later. They found him floating face down in a canal. He'd been beaten to death. He died a terrible death, very slow, very painful. Several American officials told me that the phone call ordering the murder of Saleem Shahzad came from the office of General Kayani, the head of the Pakistan Army, and thereby the country's most powerful man.

MARTIN: That was in May. Over the past five months, things haven't gotten any better for journalists.

MOSHARRAF ZAIDI: I'm in Islamabad. It's three minutes after midnight.

MARTIN: Mosharraf Zaidi is a Pakistani newspaper columnist. He actually knew Saleem Shazhad. They were distantly related by marriage. He told us he doesn't really have much to say about Saleem's death, but a lot of journalists in Pakistan, he says, don't feel safe.

ZAIDI: And there's been instances where journalists have been picked up and humiliated, harassed. Obviously, the story with Syed Saleem Shahzad is one, but, you know, we're - obviously, the intelligence community has denied any role, but there's - those whispering campaign hasn't really stopped.

MARTIN: And the big reason it's just a whisper campaign in Pakistan, instead of what might happen if, say, the CIA did something similar...

ZAIDI: The big difference is that the people that make decisions above the CIA are directly accountable to the American people. Our intelligence services, our police services, our military hasn't had a sustained period where it had to be accountable to elected officials and go through those processes to develop the - an accountability that a democracy needs to have.

FILKINS: There really is no civilian control over the military at all.

MARTIN: Again, Dexter Filkins of The New Yorker.

FILKINS: They control most of the public resources. They get the biggest slice of the budget. They do what they want. They overthrow governments when they don't like them. I was followed around when I was there. The guy from the - somebody from the ISI came by my hotel room several times. I think my phones were tapped. People who I spoke to were being threatened. I mean, that's what it's like to work there.

MARTIN: And just out of curiosity, what was the reaction to your most recent piece?

It was extremely muted. I mean, there were a couple of things in the piece that, by any measure, were big news in Pakistan, one I mentioned, about the order to kill Saleem having come from General Kayani's office.

That's pretty provocative, I'd say.

FILKINS: Yeah, that's pretty provocative. And it's not anything, frankly, that anyone could feel safe about writing in a Pakistani newspaper. And so the result of that is, as far as I could tell, there wasn't any mention of my story in any of the papers.

MARTIN: In his testimony to Congress recently, Admiral Mike Mullen said that the ISI is a, quote, "veritable arm of the Haqqani network," and that's the group waging attacks on U.S. forces across the border in Afghanistan. Based on what you've just articulated as the power structure there, was that an accurate characterization?

FILKINS: I think so. It's such a troubling picture, and it's kind of absurd in some ways. I mean, here you have - the United States is at war in Afghanistan. Pakistan is supposed to be our ally. We gave them $3 billion last year. And at the very same time, the same military and intelligence service, which gets the bulk of that American taxpayer money, is helping to kill American soldiers. But there's no easy answer. There's no quick fix.

MARTIN: You say there's no quick fix. Why?

FILKINS: Well, 85 to 90 percent of the supplies the United States sends into Afghanistan go through Pakistan. You know, Afghanistan is landlocked. There's Pakistan and there's Iran, and then in the north, you know, they'd have to come through Russia. So the Pakistanis kind of have us over a barrel, and they know that.

And the other reason, of course, is that they have about 100 nuclear weapons. And so there's a terrible fear in the American government and other places that those nukes are going to fall into the wrong hands.

MARTIN: Dexter Filkins. His recent New Yorker article about Saleem Shazhad is called "The Journalist and the Spies." Daniel Markey is a former State Department official. Now, he's with the Council on Foreign Relations. And he says Pakistan is hedging its bets.

DANIEL MARKEY: Pakistan seeks to have some influence in Afghanistan. And one of the things that it's come upon is the use of militant groups to expand its influence, those include the Haqqani network. It's not limited to the Haqqani network, though. Pakistan uses a similar tactic with respect to India where it's used Lashkair-e-Taiba, a militant terrorist organization, to project its influence there. And it's used these relationships to - so violence and instability in these other countries keep them off balance and keep its hands and its involvement inside both of these countries to project its own interests.

MARTIN: So how does the U.S. counter that? When America sees groups like the Haqqani network, like Lashkair-e-Taiba as threats and Pakistan sees them as some kind of insurance policy, how do you counter that?

MARKEY: Well, my sense, and I've felt this way for some time, is that the United States need to make it very clear that the United States is willing to take action against these groups very directly, and at the same time, the United States should open up or offer a carrot to the Pakistanis or a way for them to project their influence without using these groups. And so the kinds of assistance, both military and civilian, to Pakistan have made sense.

There are real questions now as to whether the United States can continue to offer the kind of carrots that we have in the past because the U.S. Congress is so angry about this perceived threat posed by the Pakistanis that it may cut off assistance in the near future.

MARTIN: And what would be the implication of that? I mean, we've - the United States has doled out tens of billions of dollars in military aid to Pakistan, and here we are in the fall of 2011 and our top military officer has accused the Pakistani government of supporting a group that bombed the U.S. embassy.

Yeah. It's pretty easy to see the past decade right now as having been a significant failure. I don't think it's quite as bad as that, but there are real problems. That is, we haven't been coercive enough or credible enough in the threats that we've launched to the Pakistanis that they're not convinced that we'll actually be able to take action against these groups ourselves.

And at the same time, unless we're able to show the Pakistanis that we have something that we can offer them, say, trade benefits, other types of assistance that they've been asking for, for years, I don't think we're going to get them to move off the dime.

MARKEY: I can understand we're very frustrated. There's no reason why I can possibly say that it would be necessarily appealing to provide them more in the way of assistance, but the real question is can we get them to change? And if these things might bring us plausible prospect of change, then I think we ought to try.

MARTIN: Daniel Markey is a senior fellow at the Council on Foreign Relations where he focuses on U.S. policy in South Asia. Thanks very much, Daniel. We appreciate it.

Thank you.

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