Adm. Mike Mullen retired last week after spending four years as chairman of the Joint Chiefs of Staff trying to improve relations between the U.S. and Pakistan.
In his parting remarks, he had some advice for his successor, Gen. Martin Dempsey.
"I urge Marty to remember the importance of Pakistan to all this. To try to do a better job than I did with that vexing and yet vital relationship," he said. "I continue to believe there is no solution without Pakistan and no stable future in the region without a partnership."
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.
Much of the tension is over Pakistan's Inter-Services Intelligence, the spy agency at the center of a recent piece by reporter Dexter Filkins in the New Yorker.
Filkins wrote about Syed Saleem Shahzad, a Pakistani journalist known for his exposés of the Pakistani military and the ISI. Some suspected the agency of harboring al-Qaida leader Osama bin Laden.
Filkins told weekends on All Things Considered guest host Rachel Martin that he met Shahzad at a coffee shop in the Pakistani capital, Islamabad, in May. Bin Laden had been killed that week, and Shahzad was the type of contact an American journalist like Filkins could depend on for some inside information about what happened.
Shahzad wrote a story last year when bin Laden was still alive about how the al-Qaida chief was on the move again, meeting people and crossing the border. The ISI, he told Filkins, was not a fan of his s reporting, so he got a phone call.
"So he shows up at the ISI headquarters and sits down with the generals and the admirals and they say, 'We didn't like your story last week,'" Filkins says.
The ISI told Shahzad they wanted the world to believe that bin Laden was dead, and he was making that harder.
"Now think about that, this is March, when Osama bin Laden is still alive," Filkins says. "Why on earth is the Pakistani intelligence service saying to a reporter [they] want the world to believe Osama is dead?"
Shahzad never reported what the ISI had said to him about bin Laden. Filkins pressed him for more information about Pakistan and the ISI, but says Shahzad grew increasingly nervous. He says he kept changing the subject and saying he needed to get his family out of Pakistan.
"I met a very nervous man. I mean, I met a guy who was afraid for his life," Filkins recalls.
About a week later, Shahzad wrote another article: about possible links between al-Qaida and the Pakistani navy. That article would be his last.
"He had written that piece on May 22 [and] he disappeared, I think, within a day and a half," Filkins says. "Two days later, they found him floating facedown in a canal. He'd been beaten to death. He died a terrible death; very slow, very painful."
Filkins says several American officials told him that the phone call ordering Shahzad's killing came from the office of Gen. Ashfaq Parvez Kayani, the head of the Pakistan army and thereby the country's most powerful man.
Mosharraf Zaidi, a Pakistani newspaper columnist who knew Shahzad and was a distant relation, says many journalists in Pakistan don't feel safe.
"There's been incidences where journalists have been picked up, humiliated, harassed, obviously the story with Syed Saleem Shahzad is one — where obviously the community denies any role but the whispering campaign hasn't really stopped," Zaidi says.
Zaidi says the reason it's a whisper campaign rather than a riot is that Pakistani security officials aren't accountable to the public.
"Our intelligence services, our police, military, haven't had a sustained period where it's had to be accountable to elected officials and go through those processes to develop the kind of accountability that a democracy needs to have," he says.
Filkins says there is no civilian control over the military in Pakistan.
"They do what they want. They overthrow governments when they don't like them ... you really do feel like you're living inside of a spy novel," he says.
Filkins says the difficulty in U.S.-Pakistan relations is that about 85 to 90 percent of the supplies going to Afghanistan go through Pakistan. Simply cutting Pakistan off is not an option.
"The other reason is that they have about 100 nuclear weapons and not all of which we really know the location of," Filkins says. "And there's a terrible fear that those nukes are going to fall into the wrong hands."
Next Steps For The U.S.
This past week on NPR, Pakistani Foreign Minister Hina Rabbani Khar responded to Mullen's comments, calling them "counterproductive." She said the past successes between the U.S. and Pakistan cannot be "shoved under the rug."
Daniel Markey, a former State Department official now with the Council on Foreign relations, agrees that the U.S. and Pakistan have shared success before. But he says Pakistan is hedging its bets when it comes to going after insurgent groups within its borders.
"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 their influence that includes the Haqqani network," Markey says.
The tactic – also used against neighbor and rival India — is used to sow violence and instability and project Pakistan's own interests, Markey says.
The U.S. needs to make it very clear it is unacceptable for Pakistan to use militant groups that the U.S. has identified as threats, Markey says.
"Beyond that, the U.S. should open up a way for [Pakistan] to project their influence without using these groups," Markey says.
The problem now is that there's a question of whether the U.S. can continue to offer the type of assistance it has in the past to Pakistan because of Congress' ire at the country. That anger could see assistance to Pakistan cut off in the near future.
Offering new avenues for Pakistan to raise its influence without using these militant groups is a challenge, Markey says.
Unless the U.S. offers something such as trade benefits or other types of assistance that Pakistan has requested for years, Markey says he doesn't believe the U.S. can get them to budge. The problem is making that aid appealing to those who have to approve it.
"The real question is: Can we get them to change?" Markey says. "But if these things might bring us plausible prospect of change, I think we should try."