"The Doctor At The Heart Of The U.S.-Pakistan Rift"

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The relationship between the United States and Pakistan has never been easy, but it is important. Secretary of State John Kerry sat down today with Pakistan's national security and foreign affairs adviser to talk strategy. The big themes: How to stabilize Afghanistan and what to do about a dramatic surge in deadly Taliban attacks in Pakistan.

And then, as NPR's Philip Reeves tells us, there is a very pointed dispute over one man.

PHILIP REEVES, BYLINE: It's the case of Shakil Afridi. He's the Pakistani doctor who helped the CIA track down Osama bin Laden in 2011. To most Americans, that makes him a hero. But not to most Pakistanis, says General Javed Ashraf Qazi, former head of Pakistan's intelligence agency - the ISI.

GENERAL JAVED ASHRAF QAZI: Any person who cooperates with a foreign intelligence agency is considered a traitor.

REEVES: The ISI detained Afridi after they discovered his role in the raid that killed bin Laden. The doctor's been in prison ever since. The U.S. government's repeatedly called for his release. Websites in America are collecting signatures. And now Congress is piling on pressure. Its recently passed appropriation bill says $33 million in aid to Islamabad should be withheld until Afridi's released. That's a very small sum, but it sends a signal - a signal that irks General Qazi.

QAZI: Shakil Afridi is our business. He's our citizen. So whatever we do with him, it should not be a concern of United States.

REEVES: That congressional bill also says Afridi must be cleared of all charges relating to the help he gave the U.S. in finding bin Laden. Yet the doctor's lawyers say the charge he's actually facing is entirely different. After his arrest, Afridi was tried for having alleged links with an Islamist militant group. The case was heard by a court in Pakistan's tribal belt in the mountains bordering Afghanistan. In the tribal areas, there's a separate legal system that dates back to the British Empire and is in dire need of reform, says Samina Ahmed, of the International Crisis Group.

SAMINA AHMED: The normal courts don't operate there, so you don't have the normal process. You don't have the normal protections either that the constitution offers.

REEVES: Afridi's lawyers say he wasn't even in court for his own trial and nor were they. Qamar Nadeem Afridi is on the doctor's legal team and is a relative. He dismisses the allegations against the doctor as...

QAMAR NADEEM AFRIDI: Totally false. The case is totally false and fabricated case.

REEVES: The tribal court convicted Afridi and, in May 2012, sentenced him to 33 years in jail. That sentence was later overturned. But the doctor remains behind bars awaiting a retrial, again before a tribal court. Qamar Nadeem Afridi says this should be an entirely new trial where witnesses can actually be questioned. But he fears that won't be allowed.

AFRIDI: The political authorities are not willing to restart the case, and they said that they will decide the case upon the same old file.

REEVES: Qamar Nadeem Afridi says he's had no access to the doctor since August 2012.

AFRIDI: I am not allowed to meet him. I tried several times to go to central jail and the other departments, and we requested them that I want to - as a lawyer and as a family member, I want to meet him, but they are not permitting me.

REEVES: Even if the retrial clears the doctor, his problems may well not be over. Prosecutors have told the Pakistani media that they're working on a new case, alleging he murdered a young patient some eight years ago. Over the years, the U.S.-Pakistan relationship has hit some serious bumps in the road. The dispute over Afridi is not one of these, but it is a source of friction. Islamabad says it's disappointed by Congress' plan to hold back $33 million. General Qazi argues that the move is simply counterproductive.

QAZI: Actually, you are making sure he's not released by doing that because you are humiliating Pakistan. It gives a very bad taste in the mouth.

REEVES: Philip Reeves, NPR News, Islamabad.