Aafia Siddiqui was missing for five years and reappeared in Afghanistan in 2008.

In May 2009, Petra Bartosiewicz received the first H.D. Lloyd Investigative Fund grant for her report on the case of Aafia Siddiqui, a Pakistani neuroscientist who vanished from her hometown of Karachi in 2003 along with her three children. At the time Siddiqui went missing, she was suspected by U.S. law enforcement of being an Al Qaeda operative, and the prevailing belief, at least among Pakistanis, was that she was “disappeared” by the U.S. in connection with the global war on terrorism. Then in August 2008 Siddiqui reappeared in Afghanistan, and her story grew stranger still. “The Intelligence Factory: How America Makes Its Enemies Disappear,” Bartosiewicz’s investigation of Siddiqui’s case and the phenomenon in which hundreds of individuals who have gone missing in Pakistan since the attacks of September 11, 2001, appears in the November 2009 issue of Harper’s Magazine. Her reporting on the Siddiqui case will be part of her forthcoming book on terrorism trials in the U.S., “The Best Terrorists We Could Find,” to be published by Nation Books in 2010.

This began as an essay about “how I got the story” of Aafia Siddiqui, but despite many months of reporting, I never really did “get” the story. I have no definitive answer as to where Siddiqui was during her five missing years, or who, if anyone, picked her up, or who held her, or how she ended up in Afghanistan, where she was finally captured. But I realized along the way there was another story to tell.

“The Intelligence Factory” examines how our system for apprehending terrorists has created an infinite demand for “intelligence,” which comes largely from detainees like Siddiqui. While the United States has devoted great energy to apprehending and interrogating these detainees, there are few mechanisms to determine the veracity of the intelligence being generated. The role of “intelligence” goes to the heart of a fundamental dilemma in tracking terrorism in that in almost every case the crime hasn’t happened yet. Law enforcement is looking for someone who hasn’t done the deed—they haven’t blown up a building, they haven’t hijacked a commercial airliner, they haven’t killed anyone. The danger then is that what the criminal justice system must deal with is not the subject’s alleged actions, but their suspected intentions.

I’ve covered terrorism trials in the U.S. for the past five years and Siddiqui’s case, like so many others, is at first glance a straightforward crime story. She is charged with attempted murder for shooting at a group of U.S. soldiers and FBI agents while in custody in Afghanistan. But the criminal charges elide more daunting questions. Where was she during her five missing years? Where were her children? Is she the fearsome extremist portrayed in much of the media—the Al Qaeda mom—or a woman caught in a series of far more complicated but ultimately less nefarious circumstances?

The answers make all the difference in understanding her intentions and thereby framing the criminal case in which she is now embroiled. Mind-reading, needless to say, is not supposed to be the purview of our courts. From the start I knew there was almost no chance I would interview Siddiqui herself, even though by the time I began my reporting she’d been transported to the U.S. to face indictment in a New York federal court. The Justice Department rarely allows journalists to interview defendants before trial, but even if they had, I doubt Siddiqui would have spoken with me.

In the weeks after her arrival in New York she was disoriented and in pain from a gunshot wound she’d received in Afghanistan. She didn’t want to speak to her defense attorneys, let alone a reporter, she didn’t want to appear in court, and she was deteriorating mentally, seeing apparitions in her jail cell.

So the mystery I tried to solve was why Siddiqui went missing in the first place, and this is how I came to investigate the business of intelligence gathering.

In Siddiqui’s case, as in so many others, getting to the root of the evidence against a defendant is additionally hindered, if not made impossible, by the fact that most former and current intelligence officials will only speak to reporters off the record or on background. Unnamed sources, by virtue of shielding their identity, can feed a reporter spin and misinformation with greater impunity, and in stories involving “intelligence information,” there is a greater chance this information will land unvetted in the public sphere, and readers will not know whether they are reading the truth or whether some hidden agenda is being played out.

The use of unnamed sources is a bad trend in journalism in general, one that has been exacerbated by journalists themselves, who, generally for expediency, acquiesce to it. There is a small circle of former intelligence officers willing to speak openly to the press, who are invoked repeatedly and liberally by the media (I challenge anyone to find a major national security related book in which ex-CIA officer Vince Cannistraro is not cited), and while these individuals certainly have expertise worth sharing, the pool of information about the inner workings of the intelligence community is inevitably far shallower than the coterie of talkative ex-intel officers would make it appear. Moreover, it’s become standard that government officials, including, bizarrely, those who work in the public affairs offices of the various law enforcement and intelligence branches, insist their interviews are off the record or on background.

The CIA press officer I spoke to for the Siddiqui story, George Little, was actually startled when in the middle of our one brief conversation, after we covered a series of entirely benign factchecking questions, he asked me if we were on the record. When I said yes, he quickly ended the phone call. It was against this backdrop that I had to weigh the government’s initial assertions about Siddiqui—that she was an Al Qaeda operative, that she was a potential suicide bomber, that she’d been on the run for five years, that she’d married Khalid Sheikh Mohammed’s nephew. To try to get some sense of context for Siddiqui’s life, I traveled to Pakistan this spring to meet with her family, who after years of being questioned by intelligence and law enforcement officials were understandably paranoid about speaking with a journalist. Siddiqui’s sister was convinced from the start I was employed by the CIA, and I don’t believe I was ever able to persuade her otherwise.

But over six weeks of reporting in Karachi, Lahore and Islamabad, I came to see that no matter what Siddiqui might have done, her life at the time she vanished was in turmoil and could not have helped but influence her actions. In the space of a single year she went through a bitter divorce, witnessed the death of her father, and gave birth to her third child—alone. I did not leave Pakistan with all the answers I sought, but the trip made apparent the greater political context in which her disappearance played out.

As I expected, Pakistan on the ground is far different than the mostly violent images that dominate the U.S. media, in part because the heightened risk is commonplace enough that it has become an accepted fact of life. While I was in Lahore the visiting Sri Lankan cricket team was ambushed by a team of masked gunman in the middle of the workday, but by sunset traffic had resumed to its normal flow at the shooting site.

The one place I wanted to travel to but was unable was Ghazni, Afghanistan, the scene of Siddiqui’s arrest in August 2008. Ghazni is about 150 miles south of Kabul, and the highway joining the two cities is among the most dangerous stretches in Afghanistan. Journalists braver than I have made it to Ghazni by land, but the only marginally safe way is by air, which would have required hitching a ride with a United Nations transport during one of its regular runs. There had been a number of kidnappings of foreign journalists around the time I wanted to travel, so I hired a local reporter in Ghazni to conduct a series of video interviews with police officials and residents who witnessed Siddiqui’s arrest. But as with so many other aspects of this story, the completely divergent accounts, in this case from individuals who were actual witnesses to the event, brought little clarity.

The best chance for definitive answers about what transpired in Ghazni will likely come at Siddiqui’s trial, now scheduled for January 2010. It is unlikely, however, that the bigger mysteries surrounding her disappearance will be resolved to any satisfaction. Nor will the trial address one of the most troubling aspects of Siddiqui’s story—the two youngest of her three children, Mariam and Suleiman, remain missing. Suleiman, born in Karachi and just six months old when he vanished with his mother, is suspected to be dead. Mariam, now eleven years old, was born in the U.S., making her both a citizen and a minor, and meriting an investigation by our government.

When I asked the State Department to comment on whether any effort was being made to locate her, the response was “no comment.” Then, because of Siddiqui’s pending trial I was referred to the Justice Department. When I called the Justice Department to ask about Mariam, I was informed that her disappearance has nothing to do with the criminal case and that they would have no comment either.

It’s likely that much more than the whereabouts of a child will remain a mystery.

Petra Bartosiewicz is a journalist living in Brooklyn, New York. You can reach her at www.petrabart.com. Her original article was published in Harper’s Magazine in November: “The Intelligence Factory: How America Makes its Enemies Disappear.” Bartosiewicz also wrote an opinion piece that appeared in the LA Times.

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