The Intelligence Factory

How America makes its enemies disappear.


When I first read the U.S. government’s complaint against Aafia Siddiqui, who is awaiting trial in a Brooklyn detention center on charges of attempting to murder a group of U.S. Army officers and FBI agents in Afghanistan, the case it described was so impossibly convoluted—and yet so absurdly incriminating—that I simply assumed she was innocent. According to the complaint, on the evening of July 17, 2008, several local policemen discovered Siddiqui and a young boy loitering about a public square in Ghazni. She was carrying instructions for creating “weapons involving biological material,” descriptions of U.S. “military assets,” and numerous unnamed “chemical substances in gel and liquid form that were sealed in bottles and glass jars.” Siddiqui, an MIT-trained neuroscientist who lived in the United States for eleven years, had vanished from her hometown in Pakistan in 2003, along with all three of her children, two of whom were U.S. citizens. The complaint does not address where she was those five years or why she suddenly decided to emerge into a public square outside Pakistan and far from the United States, nor does it address why she would do so in the company of her American son. Various reports had her married to a high-level Al Qaeda operative, running diamonds out of Liberia for Osama bin Laden, and abetting the entry of terrorists into the United States. But those reports were countered by rumors that Siddiqui actually had spent the previous five years in the maw of the U.S. intelligence system—that she was a ghost prisoner, kidnapped by Pakistani spies, held in secret detention at a U.S. military prison, interrogated until she could provide no further intelligence, then spat back into the world in the manner most likely to render her story implausible. These dueling narratives of terrorist intrigue and imperial overreach were only further confounded when Siddiqui finally appeared before a judge in a Manhattan courtroom on August 5. Now, two weeks after her capture, she was bandaged and doubled over in a wheelchair, barely able to speak, because—somehow—she had been shot in the stomach by one of the very soldiers she stands accused of attempting to murder.

It is clear that the CIA and the FBI believed Aafia Siddiqui to be a potential source of intelligence and, as such, a prized commodity in the global war on terror. Every other aspect of the Siddiqui case, though, is shrouded in rumor and denial, with the result that we do not know, and may never know, whether her detention has made the United States any safer. Even the particulars of the arrest itself, which took place before a crowd of witnesses near Ghazni’s main mosque, are in dispute. According to the complaint, Siddiqui was detained not because she was wanted by the FBI but simply because she was loitering in a “suspicious” manner; she did not speak the local language and she was not escorted by an adult male. What drove her to risk such conspicuous behavior has not been revealed. When I later hired a local reporter in Afghanistan to re-interview several witnesses, the arresting officer, Abdul Ghani, said Siddiqui had been carrying “a box with some sort of chemicals,” but a shopkeeper named Farhad said the police had found only “a lot of papers.” Hekmat Ullah, who happened to be passing by at the time of her arrest, said Siddiqui “was attacking everyone who got close to her”—a detail that is not mentioned in the complaint. A man named Mirwais, who had come to the mosque that day to pray, said he saw police handcuff Siddiqui, but Massoud Nabizada, the owner of a local pharmacy, said the police had no handcuffs, “so they used her scarf to tie her hands.” What everyone appears to agree on is this: an unknown person called the police to warn that a possible suicide bomber was loitering outside a mosque; the police arrested Siddiqui and her son; and, Afghan sovereignty notwithstanding, they then dispatched the suspicious materials, whatever they were, to the nearest U.S. military base.

The events of the following day are also subject to dispute. According to the complaint, a U.S. Army captain and a warrant officer, two FBI agents, and two military interpreters came to question Siddiqui at Ghazni’s police headquarters. The team was shown to a meeting room that was partitioned by a yellow curtain. “None of the United States personnel were aware,” the complaint states, “that Siddiqui was being held, unsecured, behind the curtain.” No explanation is offered as to why no one thought to look behind it. The group sat down to talk and, in another odd lapse of vigilance, “the Warrant Officer placed his United States Army M-4 rifle on the floor to his right next to the curtain, near his right foot.” Siddiqui, like a villain in a stage play, reached from behind the curtain and pulled the three-foot rifle to her side. She unlatched the safety. She pulled the curtain “slightly back” and pointed the gun directly at the head of the captain. One of the interpreters saw her. He lunged for the gun. Siddiqui shouted, “Get the fuck out of here!” and fired twice. She hit no one. As the interpreter wrestled her to the ground, the warrant officer drew his sidearm and fired “approximately two rounds” into Siddiqui’s abdomen. She collapsed, still struggling, then fell unconscious.

The authorities in Afghanistan describe a different series of events. The governor of Ghazni Province, Usman Usmani, told my local reporter that the U.S. team had “demanded to take over custody” of Siddiqui. The governor refused. He could not release Siddiqui, he explained, until officials from the counterterrorism department in Kabul arrived to investigate. He proposed a compromise: the U.S. team could interview Siddiqui, but she would remain at the station. In a Reuters interview, however, a “senior Ghazni police officer” suggested that the compromise did not hold. The U.S. team arrived at the police station, he said, and demanded custody of Siddiqui, the Afghan officers refused, and the U.S. team proceeded to disarm them. Then, for reasons unexplained, Siddiqui herself somehow entered the scene. The U.S. team, “thinking that she had explosives and would attack them as a suicide bomber, shot her and took her.”

Siddiqui’s own version of the shooting is less complicated. As she explained it to a delegation of Pakistani senators who came to Texas to visit her in prison a few months after her arrest, she never touched anyone’s gun, nor did she shout at anyone or make any threats. She simply stood up to see who was on the other side of the curtain and startled the soldiers. One of them shouted, “She is loose,” and then someone shot her. When she regained consciousness she heard someone else say, “We could lose our jobs.”

Siddiqui’s trial is scheduled for this November. The charges against her stem solely from the shooting incident itself, not from any alleged act of terrorism. The prosecutors provide no explanation for how a scientist, mother, and wife came to be charged as a dangerous felon. Nor do they account for her missing years, or her two other children, who still are missing. What is known is that the United States wanted her in 2003, and it wanted her again in 2008, and now no one can explain why.

As the “global war on terror” enters its ninth year, under the leadership of its second commander in chief, certain ongoing assumptions have gained the force of common wisdom. One of them, as Barack Obama explained in a major policy speech last May, is that we have entered a “new era” that will “present new challenges to our application of the law” and require “new tools to protect the American people.” Another, as Obama made clear in the same speech, is that the purpose of these new tools and laws is “to prevent attacks instead of simply prosecuting those who try to carry them out.” These positions are appealing, but they fail to address what might be thought of as an underlying economic disequilibrium. The continued political appetite for a global war on terror has led to a commodification of “actionable intelligence,” which is a product, chiefly, of human prisoners like Aafia Siddiqui. Because this war, by definition, has no physical or temporal boundaries, the demand for such intelligence has no limit. But the world contains a relatively small number of terrorists and an even smaller number of terrorist plots. Our demand for intelligence far outstrips the supply of prisoners. Where the United States itself has been unable to meet that demand, therefore, it has embraced a solution that is the essence of globalization. We outsource the work to countries, like Pakistan, whose political circumstances allow them to produce prisoners with far greater efficiency.

What the CIA and the FBI understand as an acquisition solution, however, others see as a human-rights debacle. Just as thousands of political dissidents, suspected criminals, and enemies of the state were “disappeared” from Latin America over the course of several decades of CIA-funded dirty wars, so too have hundreds of “persons of interest” around the world begun to disappear as a consequence of the global war on terror, which in many ways has become a globalized version of those earlier, regional failures of democracy.

Many individual cases are well known. Binyam Mohamed, an alleged conspirator in Jose Padilla’s now debunked “dirty bomb plot,” was arrested in Karachi in 2002 and flown by the CIA to Morocco, where he was tortured for eighteen months. He eventually emerged into the non-covert prison system, as a detainee at Guantánamo, and was released earlier this year without charge. Maher Arar, a Canadian citizen, was arrested at New York City’s John F. Kennedy Airport in 2002 while on his way home from a vacation, flown by the CIA to a Syrian prison, held in a coffin-size cell for nearly a year, and then released, also without charges. Saud Memon, a Pakistani businessman rumored to own the plot of land where the Wall Street Journal reporter Daniel Pearl was murdered, was arrested in 2003, held by the United States at an unknown location until 2006, then “released” to Pakistan, where in April 2007 he finally emerged, badly beaten and weighing just eighty pounds, on the doorstep of his Karachi home. He died a few weeks later.

The total number of men and women who have been kidnapped and imprisoned for U.S. intelligence-gathering purposes is difficult to determine. Apart from Iraq and Afghanistan, the main theaters of combat, Pakistan is our primary source of publicly known detainees—researchers at Seton Hall University estimated in 2006 that two thirds of the prisoners at Guantánamo were arrested in Pakistan or by Pakistani authorities—and so it is reasonable to assume that the country is also a major supplier of ghost detainees. Human Rights Watch has tracked enforced disappearances in Pakistan since before 2001. The group’s counterterrorism director, Joanne Mariner, told me that the number of missing persons in the country grew “to a flood” as U.S. counterterrorism operations peaked between 2002 and 2004. In that same three-year period, U.S. aid to Pakistan totaled $4.7 billion, up from $9.1 million in the three years prior to the U.S. invasion of Afghanistan. Correlation does not prove causation, of course, but Pakistan’s former president, Pervez Musharraf, did claim in his 2006 memoir, In the Line of Fire, that his country had delivered 369 Al Qaeda suspects to the United States for “millions of dollars” in bounties (a boast he neatly elides in the Urdu edition). It is reasonable to suspect this figure is on the low side.

One reason estimates are so inconclusive, of course, is that the business of disappearance is inherently ambiguous. Missing-person reports filed in Pakistan rarely claim that the detained individual was picked up by the CIA or the FBI. Instead, the detainee is almost always arrested by “city police” or “civilian clothed men” or unidentified “secret agency personnel” who arrive in “unmarked vehicles.” The secretary-general of the Pakistani NGO Human Rights Commission, Ibn Abdur Rehman, described the process. “A man is picked up at his house, brought to the police station,” he said. “The family comes with him and are told, ‘He’ll be released in an hour, go home.’ They come back in an hour and are told, ‘Sorry, he’s been handed off to the intelligence people and taken to Islamabad.’ After that, the individual is never heard from again. When the family tries to file a missing-person report, the police won’t take it, and no one admits to having custody of the person.” Some of the disappeared pass directly to U.S. custody and reappear months or years later at Guantánamo or Bagram air base. Others remain captives of Pakistan’s multiple intelligence agencies or are shipped to places like Uzbekistan, whose torture policies are well known. Others simply vanish, their fate revealed only by clerical errors, or when they turn up dead.

Most of the arrests and detentions take place under the auspices of Pakistan’s Inter-Services Intelligence (ISI), which the CIA helped expand in the 1980s largely in order to wage a proxy war against Soviet forces in Afghanistan (where the ISI continues to wield considerable influence). The agency has evolved into a powerful institution with its own agendas and alliances—it has long pursued ethnic separatists in the Baluchistan region, for instance, where the Human Rights Commission estimates that at least 600 individuals have disappeared—and the result is that the CIA itself often has little knowledge of the provenance or purpose of a given arrest.

Such may be the case with Siddiqui. To my knowledge, the only current or former U.S. official to comment publicly on the significance of her capture was John Kiriakou, a retired CIA officer who gained notoriety in 2007 when he told ABC News that the CIA waterboarding of Abu Zubaydah, an Al Qaeda lieutenant, produced life-saving intelligence in less than a minute. Although Justice Department memos later revealed that Zubaydah was waterboarded eighty-three times, Kiriakou’s comments did much to foster acceptance of the practice among the American public—and his description of Siddiqui seemed calibrated to achieve a similar effect. In 2008 he told ABC News, which had hired him as a consultant after his waterboarding interview, “I don’t think we’ve captured anybody as important and as well connected as she since 2003. We knew that she had been planning, or at least involved in the planning of, a wide variety of different operations.” When I called Kiriakou to ask him about those operations, though, he said the extent of his knowledge was that Siddiqui’s name “had popped up an awful lot” while he was in Pakistan searching for Zubaydah in 2002, and that “the FBI talked about her so often that I thought she must be a big fish.” After he left Pakistan, he forgot all about Siddiqui until ABC called for an interview. “I actually had to Google as to remember who she was,” he said.

Last spring, in the hope that I might discover how Siddiqui became such a sought-after commodity, I took the eighteen-hour flight from New York to Karachi. Pakistan’s cities are like many in the Third World: overwhelmed with humanity, underserved by government, and ruled by a wealthy elite who cultivate an atmosphere of lawless entitlement. The current president, Asif Ali Zardari, widower of slain former Prime Minister Benazir Bhutto, was once charged with (though not tried for) attempting to extort a Pakistani businessman by strapping a remote-controlled bomb to the man’s leg. My host in Karachi, a friend of a friend, was a charming fashion designer and gun aficionado who also happened to be a bona-fide feudal lord. The day after my arrival, as one of his servants massaged his neck, he explained to me that he could have the subjects on his lands killed, though I had the impression that he would consider such an act gauche.

Siddiqui’s own family is well known in Karachi. They are religiously conservative, but also, in certain respects, “Western.” Siddiqui’s father, who died in 2002, was a doctor educated in England. Her brother is an architect in Houston; her sister, now one of Pakistan’s premier neurologists, received her training at Harvard. Siddiqui herself attended MIT as an undergraduate, and earned her doctorate in neuroscience at Brandeis. Her education, and the privilege it implies, is part of what made her disappearance so newsworthy. Families like hers are understood to have enough connections, or at least enough hired guards, to prevent their members from being kidnapped, even by the government.

The national press nonetheless seems to take for granted that Siddiqui and her children were abducted by Pakistani intelligence in 2003, most likely at the behest of the United States. Almost no one I spoke to in Karachi believed she could have remained underground and undetected by the ISI for five days, let alone five years. But there was one important exception. A few days before I arrived, Siddiqui’s ex-husband, Amjad Khan, told a reporter from the Pakistani daily News that he thought she was an “extremist” and that of course she had been on the run. This so infuriated Siddiqui’s sister, Fowzia, that she later called a press conference of her own and told reporters Khan was an abusive husband and father, and that if anyone was an extremist it was him.

Khan now lives in Karachi with his new wife and their two children, in the well-appointed home of his father, a retired businessman. He is thirty-nine years old, tall and slender, and when we met he was wearing the long beard that denotes his strict devotion to Islam. He invited me into the drawing room and signaled a servant to bring cookies and cold glasses of lassi, a yogurt drink. Khan came to know Siddiqui, he said, in 1993. She was an active supporter of Islamic causes at MIT, and during a visit to Karachi, Khan’s mother arranged for her to come to their home and give a talk on the plight of Bosnian Muslims. After the talk, Khan’s mother, presumably impressed, asked him if he liked what he saw. He said yes, and the parents arranged a wedding. The ceremony took place over the phone while Khan was in Karachi and Siddiqui already back in Boston, but Khan, who had studied medicine in Pakistan, soon followed her and took a research position at Massachusetts General Hospital.

Khan said he loved Siddiqui in the early years of their marriage but that the relationship was always somewhat volatile; he casually described an incident in which he threw a baby bottle at Siddiqui’s face and she had to go to the hospital to get stitches. The marriage began to unravel, he said, after the attacks of September 11, 2001. Siddiqui, shaken by the U.S. reaction to the attacks, flew with the children to Karachi soon after, and when Khan joined them in November, he says, Siddiqui’s “extreme nature” became apparent. She wanted him to go with her to Afghanistan to serve as a medic for the mujahedeen. When he refused, he said, “she became hysterical. She started pounding on my chest with her fists. She openly asked for a divorce in front of my family.” Khan’s parents urged him to return to Boston without Siddiqui, to complete his board exams, which he did. In January 2002, he convinced Siddiqui to return to Boston, where they patched things up sufficiently that Siddiqui became pregnant with their third child.

Then, in June 2002, the couple received a visit from the FBI. The agents said they were following up on a suspicious-activity report from Fleet Bank in Boston. Why had someone at the Saudi embassy in Washington wired $70,000 to accounts linked to their address? And why had Khan recently purchased night-vision goggles, body armor, and, according to Khan, as many as seventy military manuals, among them Fugitive, Advanced Fugitive, and How to Make C-4? “I asked the FBI,” he said, “whether I should return some of the objectionable books, and the agent replied, ‘No, we are a free country. You are free to read these books.’” Khan told me that the “night-vision goggles” were actually just a single night-vision scope for his hunting rifle; the “body armor” was a bulletproof vest for his uncle, a big-game hunter in Karachi. The $70,000 was not for them. It had been sent to a Saudi man who sublet Khan’s first Boston apartment in 2001 after the couple had moved to another place—the money was to pay for medical treatment for his son. And the military manuals, Khan explained, less convincingly, were an appeasement gift for Siddiqui. “By that time I knew the marriage wasn’t going to last,” he said. “But I had my exams coming up and needed to keep things neutral.”

The arguments continued, however, and in the end it was Khan who, in August 2002, finally demanded a divorce. The parting was quite bitter, and perhaps not entirely because of Siddiqui’s purported radical proclivities. Even before the divorce was finalized that October, Khan had contracted a marriage with his current wife, an act that Siddiqui, according to divorce papers her sister gave me, said was done “without her consent or prior knowledge.” And although Khan said he offered to pay child support and sought to see the children, the divorce papers note that he gave up permanent custody and would “have no right of any nature with the children.” He has never seen his son, Suleman, who was born that September.

Khan said he learned that Siddiqui was missing only when the FBI issued an alert in March 2003, five months after the divorce was finalized, seeking both of them for questioning. He told me he cleared his own name several weeks later in a four-hour joint interview with the FBI and the ISI, and that his “contacts in the agencies” informed him that Siddiqui had gone underground. He had no idea where his children were, he said—a claim he would later contradict. He said he and his driver saw Siddiqui in a taxi in Karachi in 2005. But they did not follow her.

As we talked, Khan’s father came and sat down and soon began answering questions for his son, who deferred to him. Eventually the father decided the interview had gone on long enough, and so Khan walked me outside, where his two young daughters from his second marriage were playing on the lawn. One was named Mariam, the same name as his daughter with Siddiqui. I asked if he had given up on the possibility of the first Mariam coming home. Khan shrugged and said he just liked the name.

Fowzia lives in Gulshan-e-Iqbal, an affluent enclave of palm trees and high-walled compounds not far from Amjad Khan’s home. When I called, she was about to hold her press conference and told me to come right over. “I got a video of the prison strip search,” she said. “It’s really gruesome.”

I knew Siddiqui had been searched when she left her holding cell for preliminary hearings. She was still recovering from her gunshot wounds and had found the process, which included a cavity search, to be humiliating and extremely painful. I assumed Fowzia had somehow acquired a tape of the search. Images of a devout Muslim woman being stripped in the presence of Western prison guards would be offensive and inflammatory, and thus newsworthy, and could help Fowzia gain sympathy for her sister’s cause.

Several TV satellite trucks were idling outside the house when I arrived, and in the living room three dozen reporters were watching the video, which Fowzia played on her laptop computer. I leaned in to get a better look and saw that it was indeed a strip search. But the woman was not Siddiqui. The video, taken from a U.S. television report on an entirely unrelated case, was meant to depict what Fowzia’s sister might have gone through—not an outright deception but a well-timed ploy to shift attention away from the damaging claims of an angry ex-husband.

After the reporters left, we sat down to discuss the case in greater detail. Fowzia kept steering the conversation away from questions about her sister’s culpability and the whereabouts of her niece and nephew. Instead, she wanted to discuss Khan’s perfidy. “He’s on a lying spree,” she said. “Let him continue!” Fowzia speculated that Khan was inventing tales about Siddiqui in order to save himself from prosecution, that he was a criminal who had been turned into an informant, that he could be trusted by no one. I asked her what proof she had that Khan had been involved in terrorist activities. She said she had none. But he certainly held extremist views, she said, and as evidence she produced a copy of the couple’s divorce agreement and directed me to a proviso that Khan had inserted: “Under no circumstances would the children be admitted in any of the schools which render education in Western style or culture.”

Fowzia’s resignation about the missing children puzzled me, as had Khan’s. When I asked her about it, she said, “I’ve coped by assuming the kids are dead.” A few years ago, she explained, a Pakistani intelligence agent had come to her house and told her that Suleman, who had been born prematurely and was sick at the time Aafia disappeared, had died in custody. I asked her who the agent was, but she said he refused to give his name. (After I left Pakistan, Khan emailed me to say he had received “confidential good news” from the ISI that Mariam and Suleman were “alive and well” with Fowzia. When I asked if he could tell me more, he wrote back that he possessed “a lot of detailed information” about his children and implied they had been with the Siddiqui family all along, but he refused to provide any of that information “because I was forbidden by the agencies/my lawyer to do so for my own safety.” Fowzia says she still has not seen the children.)

On my way out of Fowzia’s house, I passed a boy who was watching television. It was Siddiqui’s eldest son, Ahmad, now twelve years old. After his arrest at the market in Afghanistan he had again vanished, and for a month U.S. authorities denied any knowledge of his whereabouts. In fact, he had been turned over to an Afghan intelligence agency, which held him for six weeks and finally sent him to Pakistan to live with his aunt. I waved to Ahmad. He said hello and then went back to the Bollywood film he was watching. “He hasn’t talked in great detail about where he was,” Fowzia said. “He tries to figure out what answer you want him to give and he gives that answer.”

What most of us understand as human relationships, infinitely varied and poignant with ambiguity, criminal investigators understand simply as a series of associations. The mapping of “known associates” is an old and powerful investigative technique. But within the context of the global war on terror, the technique—known variously as “social-network analysis,” “link analysis,” or “contact chaining”—has been used less for solving crimes and more for preventing them. Using large computer arrays and the kind of automated data analysis that already dominate the world of global finance, investigators cobble together every scrap of available information in order to create what they hope is a picture not of a single true past but of an infinite variety of theoretical futures. In such a system, the universe of possible associations—and therefore the universe of possible detainees—also becomes unlimited. When the FBI detained more than a thousand Muslim immigrants in 2001, for instance, it provided judges at secret detention hearings an affidavit explaining that “the business of counterterrorism intelligence gathering in the United States is akin to the construction of a mosaic” and that evidence “that may seem innocuous at first glance” might ultimately “fit into a picture that will reveal how the unseen whole operates.” The FBI reasoned that even the possessors of this intelligence might not be aware of the significance of what they knew, and so they could be detained simply because the agency was “unable to rule out” their value.

It was precisely such a mosaic, in which none of the myriad connections were quite intelligible but all were laden with vague significance, that set off alarms at the FBI and CIA in the months leading up to the moment Siddiqui disappeared in 2003. In early 2002, the FBI became aware of a United Nations investigation into Al Qaeda financing that mentioned Siddiqui. A “confidential source” claimed he had “personally met” her in Liberia, where she was on a mission to “evaluate diamond operations” for her Al Qaeda bosses in Pakistan. Dennis Lormel, an FBI agent who was investigating terrorism financing at the time, told me the agency quickly debunked this specific claim. Nonetheless, the notion that Siddiqui was involved in money laundering had entered the picture.

Then, in late December 2002, two months after her divorce, Siddiqui flew from Pakistan to the United States, where she had a job interview at a hospital in Baltimore. On December 30, she made her way to nearby Gaithersburg, Maryland, and opened a post office box. She listed as a co-owner of the box a man named Majid Khan, whom she falsely identified as her husband. According to court records, the FBI began to monitor the box almost immediately.

On March 1, 2003, intelligence agents in Pakistan arrested Khalid Sheikh Mohammed, the alleged operational planner of the September 11 attacks. U.S. interrogators quickly elicited from him the names of dozens of possible co-conspirators. Among them was Majid Khan. Mohammed said he had assigned Khan to deliver “a large sum of money” to Al Qaeda.

On March 5, the ISI arrested Khan, along with his pregnant wife. According to a statement by Khan’s father, “U.S. and Pakistani agents, including FBI agents,” interrogated his son for at least three weeks at a secret detention center in Karachi. What Khan told his captors is not publicly known, but by March 18 the FBI was alarmed enough to issue a bulletin seeking Siddiqui and her ex-husband for questioning.

On March 28, FBI agents in New York City detained a twenty-three-year-old man named Uzair Paracha, who had just arrived there from Pakistan to help his father sell units of a beachfront property in Karachi. His father also owned an import/export business in Manhattan, and Paracha worked from an office there. Khalid Sheikh Mohammed had planned to use the company, he told investigators, “to smuggle explosives into the United States.” Among the first questions agents in New York asked Paracha was whether he knew Majid Khan. He said he did. And there was more: he also had the key to his post office box.

At some point that same month, Siddiqui disappeared. Her family would not, or could not, give me a specific date. The last traces of her I found came from news accounts. On March 28, the day the FBI detained Paracha, the Pakistani daily Dawn reported that local authorities took Siddiqui “to an undisclosed location” for questioning and that “FBI agents were also allowed to question the lady.” Three weeks later, on April 21, a “senior U.S. law enforcement official” told Lisa Myers of NBC Nightly News that Siddiqui was in Pakistani custody. The same source retracted the statement the next day without explanation. “At the time,” Myers told me, “we thought there was a possibility perhaps he’d spoken out of turn.”

There was one final association to take into account. On April 29, the Pakistani authorities arrested Ammar al Baluchi, a computer technician they suspected was plotting to bomb the U.S. embassy in Pakistan. Baluchi was the nephew of Khalid Sheikh Mohammed. The FBI and the CIA suspected that he had provided the 9/11 hijackers with almost a quarter of their financing. They had also come to believe, as was later reported in an undated Department of Defense “detainee biography,” that Baluchi had “married Siddiqui shortly before his detention.”

The means by which we assemble such intelligence have become more sophisticated and also more violent. During his initial month of detention, Mohammed was waterboarded 183 times. Khan’s father claims that his son was forced “to sign a statement that he was not even allowed to read,” and Khan later attempted suicide, twice, by chewing through an artery in his arm.

The interrogations yielded a great deal of data, but it is unclear how useful any of that data actually was. Mohammed later said, “I gave a lot of false information in order to satisfy what I believed the interrogators wished to hear.” Paracha told many contradictory stories, and Baluchi, who had maintained his innocence during his U.S. military tribunal hearing, later filed a statement saying, in effect, that he was proud of his involvement in the September 11 attacks.

The roles Siddiqui and Paracha played in the post-office-box affair may have been entirely innocent. Majid Khan said at his own military tribunal hearings that his travel documents had expired while he was in Karachi and he wanted to renew them. He asked his friend Baluchi to enlist Siddiqui and Paracha to help maintain the ruse that he was still in the United States by establishing a mailing address. Khan and Baluchi both contended at Paracha’s trial that he was ignorant of their ties to Al Qaeda.

Such intelligence may actually be worse than useless. In a 2006 Harvard study of the efficacy of preemptive national-security practices, Jessica Stern and Jonathan Wiener note that “taking action based only on worst-case thinking can introduce unforeseen dangers and costs” and propose that “a better approach to managing risk involves an assessment of the full portfolio of risks—those reduced by the proposed intervention, as well as those increased.” Rather than understanding all intelligence as actionable, they write, “decision makers” should create “mechanisms to ensure that sensible risk analysis precedes precautionary actions.” At the moment, no such mechanisms appear to exist. The leader of one FBI conterterrorism squad recently told the New York Times that of the 5,500 terrorism-related leads its twenty-one agents had pursued over the past five years, just 5 percent were credible and not one had foiled an actual terrorist plot. But the gathering of intelligence continues apace.

As I traveled from Karachi to Lahore to Islamabad, questioning family members, lawyers, and spies, I heard every possible story about Aafia Siddiqui. She was a well-known extremist. She was an innocent victim. She was an informant working for the United States or Pakistan or both sides at once. Most people continued to believe that she had been arrested by someone in 2003, but it was proving impossible to determine who actually apprehended her, or who ordered the arrest, or why. I interviewed an attorney in Lahore who swore he had seen a cell-phone video of the arrest that showed what he believed was a female CIA officer slapping Siddiqui across the face. And as to her whereabouts before the arrest, the most persistent account—that she was held by the U.S. military in Bagram prison in Afghanistan—emerged from the testimony of two former detainees, one of whom, Moazzam Begg, was not even at Bagram during the years Siddiqui was missing.

One afternoon in Islamabad I met a recently retired senior Pakistani intelligence officer who had promised, if I agreed not to name him, to answer all of my questions. We spoke at his home, a gated mansion in one of the city’s wealthiest precincts. He had silver hair and a silver mustache, and he wore a gold pinky ring fitted with a large green stone. When I called to arrange the interview, he initially said he did not know why Siddiqui had disappeared. But he had since then contacted a friend at one of Pakistan’s intelligence agencies, “a very good chap” who had been “pretty senior in the hierarchy” when Siddiqui disappeared in 2003. Now, over the customary drinks and cookies, the retired intelligence officer recounted their conversation, the upshot of which was that Siddiqui had in fact been picked up by Pakistani intelligence and delivered to “the friends,” which was shorthand, he said, for the CIA.

“You people didn’t have the decency to tell me she’d been picked up?” he’d asked his colleague, referring to the jurisdictional problems that plague intelligence agencies around the world. “No, no, it was very sudden,” the colleague replied. “The friends, they were insisting.” My host told me that such insistence was irritating and disrespectful. “It was very difficult, very embarrassing for us to turn her over to you,” he said. “The decision was made at the highest levels. Bush and Musharraf likely would have known about it. After two to three days, we passed her along to the CIA.”

By the time our meeting ended, I was convinced that I had heard the definitive account if not of Siddiqui’s reappearance then at least of her disappearance—until, after a fifteen-minute taxi ride later to a less fashionable neighborhood, I arrived at the home of Siddiqui’s elderly maternal uncle, Shams ul Hassan Faruqi, a geologist. As we sat in his home office, surrounded by maps and drawings of rock strata, Faruqi told an entirely different story. He said Siddiqui showed up at his house unannounced one evening in January 2008, a time when, according to the intelligence officer I had just left, she was supposedly in the hands of the CIA. Her face had been altered, Faruqi said, as if she had undergone plastic surgery, but he knew her by her voice. She said she had been held by the Pakistanis and the Americans and was now running operations for both of them against Al Qaeda. She had slipped away for a few days, though, because she wanted him to smuggle her across the border into Afghanistan so she could seek sanctuary with the Taliban, members of which Faruqi had known from his years of mineral exploration.

A few days later I heard yet another account, this one from Ahmed Rashid, a Pakistani reporter who has been writing about the Taliban and the ISI for thirty years. As I interviewed him, we were joined by his three golden Labradors, who had just been shaved bare to make the heat more tolerable for them. Rashid told me that he, too, had heard from his sources that the Pakistanis had picked up Siddiqui. But instead of handing her directly to the CIA, they hung on to her. “It’s possible there were some conditions being laid for her being released which the Americans didn’t want to meet. So we held her for a long time,” he said. “I think she was used as a bargaining chip for something completely different which we were pissed off about.”

Perhaps the most believable account came from Ali Hasan, senior South Asia researcher for Human Rights Watch, whom I visited at his home in Lahore. “My professional view,” he said, “is they’re all lying. Siddiqui’s family is lying, the husband is lying, the Pakistanis are lying, the Americans are lying, for all I know the kids are lying. And because they’re all lying the truth is probably twenty times stranger than we all know.”

One of the chief conveniences of outsourcing is that certain costs are externalized. Pollution, for instance, is expensive. Manufacturers that pollute in the United States are required to bear its cost by paying a fine. If they outsource to a country where the cost of the pollution is borne directly by the people, they make more money. Such a transfer is obviously desirable from the point of view of the manufacturer, but it often generates political unrest in the host country, for reasons that are equally obvious. This phenomenon applies as well when the external cost of manufacturing intelligence is paid in freedom. The governments that did the outsourced work of U.S. intelligence agencies in previous dirty wars—in Argentina and Chile, Guatemala and Uruguay—eventually were toppled by popular protest, in large part because the people became aware that their leaders had profited from their suffering. Pakistanis today appear no less aware that this type of transaction is occurring in their country. Indeed, a recent poll found that the only nation they find more threatening than India, whose nuclear missiles point directly at them, is the United States. And they have begun to hold their leaders accountable for the association.

The rising number of disappearances became a decisive political issue in 2007, after Pakistan’s Supreme Court, under its chief justice, Iftikhar Chaudhry, opened hearings on behalf of the missing, demanding that they appear before the court. This initiative turned up the locations of 186 disappeared persons, many of whom were found in known Pakistani detention centers, including Imran Munir, a Malaysian of Pakistani origin who had been missing since 2006. During Munir’s hearing, it came to light that Pakistani security agents had continued trying to hide him even after the court demanded his presence. Chaudhry’s efforts to locate the disappeared were met with considerable resistance from the government. In March 2007, the chief justice himself was summoned to appear before Musharraf, where, with ISI and military chiefs present, he was ordered to resign. Chaudhry refused, and so Musharraf charged him with misconduct and suspended him from office.

In July 2007, a panel of thirteen judges reinstated Chaudhry, who quickly returned to his investigation of the disappeared. This time, he warned, he would order the heads of the security agencies themselves to testify. He also summoned Imran Munir once again, but before Munir could appear, Musharraf declared a state of emergency and put Chaudhry under house arrest. Lawyers around Pakistan, horrified to see the chief justice so flagrantly humiliated, rose up to demand his reinstatement. The Lawyers’ Movement, as it came to be known, was soon embraced by hundreds of thousands of Pakistani citizens, who marched in massive protests, and Musharraf, in the end, was the one who had to resign.

The current president, Asif Ali Zardari, gained considerable momentum in his election campaign by pledging to reinstate Chaudhry. But once in office, he hesitated to follow through on that pledge, likely because he was concerned that the court would reopen a series of corruption cases against him. The marches grew larger, though, and on March 16, 2009, while I happened to be in Pakistan, Zardari finally reinstated Chaudhry, along with several other similarly deposed justices.

I joined the hundreds of supporters gathered at the chief justice’s house in Islamabad. Families came with children, people waved placards that bore Chaudhry’s image, and a marching band with bagpipes played. Chaudhry had always maintained that his struggle was legal, not political, but the scene had all the markings of a post-campaign victory celebration. I made my way along the receiving line until I reached Chaudhry, who was surrounded by the leaders of the Lawyers’ Movement. He had been shaking hands for several hours, but I thought I would try to ask a question. When I reached him, I took his hand and asked him when he planned to take up the missing-person cases with which his name had become synonymous. He paused, as if parsing the political consequences of his answer. “I don’t know,” he finally said, and giggled uncomfortably as his handlers, looking equally uncomfortable, hustled me down the line.

It is the shooting, oddly enough, that has generated the most detailed evidence about Siddiqui’s present circumstances. After the confrontation in Ghazni, she was choppered by air ambulance to the Craig Joint Theater Hospital at Bagram air base—the same base, of course, where she may or may not once have been a prisoner. Her medical intake record notes that she was a three on the fifteen-point Glasgow Coma Scale, meaning she was almost dead. The surgeons opened her up from breastbone to bellybutton, searching for bullets. They cut out twenty centimeters of her small intestine. They also gave her transfusions of red blood cells and fresh frozen platelets and dosed her with clotting medication, which suggests she had experienced heavy blood loss. “FBI agents in room with patient at all times,” the medical record stated. “Patient is in four-point restraints.” In the span of just two weeks she went from near clinical death to being deemed “medically stable and capable of confinement.” The doctor witnessed every detail of her recovery. “Details of pertinent medical findings: Very thin, sallow coloring, dry cracked lips,” and also “flat affect, crying at times.”

From that point forward, however, the clarity of medical detail is clouded by legal concerns. Siddiqui had no lawyer during her two weeks at Bagram or on her flight to the United States. The day after she landed, she was in a Manhattan courtroom, facing charges of attempted murder. In allowing her to be transported to the United States without even a consular visit, her own government, notwithstanding its public pronouncements of support and calls for repatriation, effectively gave her up without a fight. The Pakistani embassy eventually hired a team of three attorneys to augment her two existing public defenders, but Siddiqui refused to work with them. During a prison phone call in June, she told her brother, “I just protest against this whole process and don’t want to participate.”

The only people Siddiqui seemed to trust, strangely, were the FBI agents who sat by her bedside at Bagram, and whose presence she repeatedly requested in the apparent belief that if only she could speak to them for a moment she could clear everything up. According to notes taken by the agents, she was voluble during those early days of her detention in Afghanistan. She said she “made some bad decisions in the past, but mostly did so out of naivety.” In contrast to her later statements, she confirmed that she was married to Ammar al Baluchi, whom she met when his sister rented a room at her mother’s house, and that Baluchi had asked her to help his friend Majid Khan with his immigration problem. She admitted having possession of chemicals including sodium cyanide at the time of her capture, though “not for nefarious purposes,” and she said that she had been “in ‘hiding’ for the last five years” and “aware that various law enforcement agencies had been looking for her.” She had little to say about her children. “She finds it easier to presume them dead,” the agents noted. She also volunteered to become a U.S. intelligence “asset” in the hope that she could find the “truth to the inner depths.”

It is uncertain what the defense’s theory of the case will be when Siddiqui goes on trial this November. Perhaps, as one of her lawyers told me, she never even touched the gun. Perhaps she acted in self-defense. Or perhaps, as another of her lawyers claimed at an early hearing, “she’s crazy.” In this last matter, ambiguity is once again the rule. Four prison psychiatrists examined Siddiqui. Two of them determined she was malingering, the faked illness being insanity. A third said she was delusional and that her behavior was “diametrically opposed to everything we know about the clinical presentation of malingerers,” and the fourth psychiatrist initially diagnosed her as depressive—and possibly psychotic—but later switched to the malingering camp. Siddiqui’s own contribution to the debate came in the form of a rambling letter, written last July to “All Americans loyal to the U.S.A.,” in which she proclaimed her innocence, decried the propaganda being spun against her by the “Zionist-controlled U.S. media,” and alleged that she spent years in a prison “controlled by the ‘Americans,’ of the kind that control the U.S. media.” Later that month the court ruled that she “may have some mental health issues” but that she was fit enough to stand trial.

Aafia Siddiqui is not presently charged with any act of terrorism, nor is she accused of conspiring with terrorists or giving comfort to terrorists. Her trial is unlikely to yield satisfactory answers about where she was, who picked her up and why, or even who she really is. Maybe she was working for the United States, or Pakistan, or maybe she was just in the United States looking for a job and committed a minor bit of immigration fraud that catalyzed a violent farce. One FBI official told _U.S. News & World Report _in 2003, “There’s a distinct possibility she was just a victim.” Perhaps Aafia Siddiqui is guilty of nothing more than poor choice in men. We simply do not know, and the system in which she has found herself ensures that neither will her captors.

The person who seemed best able to explain what really happened to Siddiqui, her sister, Fowzia, remained elusive until my last day in Pakistan. At our first meeting she had promised to pull together all sorts of evidence of her sister’s innocence, but by the time she finally agreed to meet again, my bags were packed and my plane just hours from departure.

She said she avoided me all these weeks because she’d been told by “multiple people” that I worked for the CIA. “All you want are documents,” she said. “I just want someone who can listen.” Then she dragged out a family photo album and started showing me pictures of her sister with various animals: goats, a camel, the family cat. “Aafia loved animals,” she said.

Then she opened a more formal binder. She flipped to a grainy photocopy of a woman lying on a bed. The woman bore a striking resemblance to Siddiqui, only she looked younger and softer, as if she’d been airbrushed; sitting at her bedside was a young man—Fowzia wouldn’t say who—and mounted on a wall behind her was what appeared to be the seal of the United States government. The seal, Fowzia said, proved the picture was taken in Bagram, but she wouldn’t say why it proved this, and before I could inspect the image any further she flipped the page and wouldn’t let me look at it again. “I’d love it if a real investigator would come and devote himself to the case,” she said. “You know, really work on it.”

Petra Bartosiewicz is a writer living in Brooklyn. Her last story for Harper’s Magazine, “I.O.U. One Terrorist,” appeared in the August 2005 issue.