On May 30th, as the sun beat down on the plains of eastern Pakistan, a laborer named Muhammad Shafiq walked along the top of a dam on the Upper Jhelum Canal to begin his morning routine of clearing grass and trash that had drifted into the intake grates overnight. The water flow seemed normal, but when he started removing the debris with a crane the machinery seized up. He looked down and saw, trapped in the grates, a human form.

Pakistani intelligence officials warned Shahzad to curb his reporting, which revealed links between the military and Al Qaeda. Illustration by SEAN MCCABE

Shafiq called some colleagues, and together they pulled out the body. Occasionally, farmers and water buffalo drown in the canal, float downstream, and get stuck in the grates, but never a man in a suit. “Even his tie and shoes were still on,” Shafiq told me. He called the police, and by the next day they had determined the man’s identity: Syed Saleem Shahzad, a journalist known for his exposés of the Pakistani military. Shahzad had not shown up the previous afternoon for a television interview that was to be taped in Islamabad, a hundred miles to the northwest. His disappearance was being reported on the morning news, his image flashed on television screens across the country. Meanwhile, the _zamindar—_feudal lord—of a village twenty miles upstream from the dam called the police about a white Toyota Corolla that had been abandoned by the canal, in the shade of a banyan tree. The police discovered that the car belonged to Shahzad. Its doors were locked, and there was no trace of blood.

The previous afternoon, Shahzad had left his apartment, in the placid F-8/4 neighborhood of Islamabad, and driven toward Dunya studios, about five miles away. It was five-thirty; the television interview was scheduled for six. According to a local journalist who talked to a source in one of Pakistan’s cell-phone companies, Shahzad’s phone went dead twelve minutes later. His route passed through some of the country’s most secure neighborhoods, and no one had reported seeing anything suspicious. Some Pakistanis speculated that Shahzad might even have known the people who took him away.

It was a particularly anxious time in Pakistan. Four weeks earlier, American commandos had flown, undetected, into Abbottabad, a military town northwest of Islamabad, and killed Osama bin Laden. The Pakistani Army, which for more than sixty years has portrayed itself as the country’s guardian and guide, was deeply embarrassed: either it had helped to hide bin Laden or it had failed to realize that he was there. Certainly it hadn’t known that the Americans were coming.

Less than three weeks after the Abbottabad raid, the Army was humiliated a second time. A group of militants, armed with rocket-propelled grenades and suicide vests, breached one of the country’s most secure bases, the Pakistan Naval Air Station-Mehran, outside Karachi, and blew up two P-3C Orion surveillance planes that had been bought from the United States. At least ten Pakistanis affiliated with the base died. The components of several nuclear warheads were believed to be housed nearby, and the implication was clear: Pakistan’s nuclear arsenal was not safe. In barracks across the country, military officers questioned the competence of Pakistan’s two most powerful men, General Ashfaq Parvez Kiyani, the chief of the Army staff, and General Ahmad Shuja Pasha, the chief of the Inter-Services Intelligence agency, or I.S.I. Some officers even demanded that the Generals resign. Ordinary Pakistanis, meanwhile, publicly disparaged the one institution that, until then, had seemed to function.

Amid this tumult, Shahzad wrote a sensational story for Asia Times Online, the Web site that employed him, saying that the attack on the Mehran base had been carried out by Al Qaeda—not by the Pakistani Taliban, which had claimed responsibility. He said that the Mehran assault had been intended to punish the military for having conducted “massive internal crackdowns on Al Qaeda affiliates within the Navy.” A number of sailors had been detained for plotting to kill Americans, and one “was believed to have received direct instructions from Hakeemullah Mehsud”—the chief of the Pakistani Taliban. It was not the first time that Shahzad had exposed links between Islamist militants and the armed forces—a connection that Pakistan’s generals have denied for years. But the Mehran article was his biggest provocation yet.

Shahzad, whose parents migrated from India after Partition, making him a muhajir—Urdu for “immigrant”—was an affable outsider within Pakistan’s journalistic circles. Asia Times Online is not connected to any of the country’s established newspapers; its editorial operations are based in Thailand. Shahzad had no local editor to guide him or restrain him. Only a few other journalists had written as aggressively about Islamist extremism in the military, and not all of them had survived.

A hallmark of Shahzad’s reporting was that it frequently featured interviews with Islamist militants, including Al Qaeda fighters. His work was sometimes inaccurate, but it held up often enough so that other journalists followed his leads. Perhaps because he had cultivated so many militants as sources, he occasionally seemed to glorify the men who were carrying out suicide bombings and assassinations. In 2009, he published a breathless account of a meeting with Ilyas Kashmiri, a top Al Qaeda leader. Shahzad noted that the terrorist “cut a striking figure,” was “strongly built,” and had a powerful handshake, adding, “Ilyas, with his unmatched guerrilla expertise, turns the strategic vision into reality, provides the resources and gets targets achieved, but he chooses to remain in the background and very low key.” At other times, like many Pakistani journalists, he seemed to spare the intelligence services from the most damning details in his notebooks. But on several important occasions—as in the case of the Mehran attack—he wrote what appeared to be undiluted truth about the Pakistani state’s deepest dilemmas.

An autopsy report showed that Shahzad had died slowly and painfully, his rib cage smashed on both sides, his lungs and liver ruptured. Someone, apparently, had intended to send a message by killing him.

The media in Pakistan immediately suggested a culprit. According to the newspaper Dawn, it was believed that Shahzad “had been picked up by the I.S.I. because of his recent story on the P.N.S.-Mehran base attack.”

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Two days after Shahzad’s body was found, an I.S.I. official made a statement denying that its agents had played any role in the killing. Shahzad’s death, he said, was “unfortunate and tragic,” adding, “Baseless accusations against the country’s sensitive agencies for their alleged involvement in Shahzad’s murder are totally unfounded.” Forty-six journalists have been killed in Pakistan since 2001, and the I.S.I. had never before issued such a stark denial. The statement hardly quieted suspicion; in fact, it heightened it. “Everybody knows who did it,” Muhammad Faizan, a colleague of Shahzad’s at Asia Times Online and a friend, told me. “But no one can say.”

I met Saleem Shahzad nine days before he disappeared, and he seemed to know that his time was running out. It was May 20th, and Islamabad was full of conspiracy theories about the Abbottabad raid: bin Laden was still alive; Kiyani and Pasha had secretly helped the Americans with the raid. Mostly, the public radiated anger and shame.

I had called Shahzad to discuss a pair of stories he’d written about bin Laden. In March, five weeks before the raid in Abbottabad, Shahzad claimed that bin Laden had suddenly come across the radar screens of several intelligence agencies: he was on the move. The story also reported that bin Laden had held a strategy meeting with an old friend, Gulbuddin Hekmatyar, an Afghan mujahideen whom the State Department considers a “global terrorist.” Then, just after the Abbottabad raid, Shahzad published a report claiming that the Pakistani leadership had known that the Americans were planning a raid of some sort, and had even helped. What the Pakistanis didn’t know, Shahzad wrote, was that the person the Americans were looking for was bin Laden. Both stories struck me as possibly dubious, but it was clear that Shahzad had numerous sources inside Pakistani intelligence and other intelligence agencies in the region.

Shahzad and I agreed to meet at a Gloria Jean’s coffee shop, not far from his home. For years, Islamabad was a sleepy town of bureaucrats; however dangerous the rest of Pakistan was, the capital was usually quiet. This was no longer true. In 2008, the Marriott Hotel, only a few miles from Gloria Jean’s, was destroyed by a suicide bomber, who killed or wounded more than three hundred people. Lately, the Kohsar Market—the collection of expensive boutiques where the Gloria Jean’s is situated—had been declared off limits for American Embassy personnel on weekends, out of fear that it would be attacked.

Shahzad and I took our coffees upstairs. He pointed to a table in an alcove by a window. “Welcome to my private office,” he said, with a smile. “No one will be able to hear us here.”

We talked for a few minutes about the Abbottabad raid and the stories he’d written. Shahzad was tall and self-possessed; he had thick black hair and a round face offset by a trim beard. He was warm and expressive, the sort of reporter whom people talked to because he seemed genuinely nice. No wonder he got all those scoops, I thought. He was wearing Western clothes and spoke flawless English. He told me that he knew some of my colleagues, and offered to help me out in any way that he could.

And then Shahzad changed the subject. What he really wanted to talk about was his own safety. “Look, I’m in danger,” he said. “I’ve got to get out of Pakistan.” He added that he had a wife and three kids, and they weren’t safe, either. He’d been to London recently, and someone there had promised to help him move to England.

The trouble, he said, had begun on March 25th, the day that he published the story about bin Laden’s being on the move. The next morning, he got a phone call from an officer at the I.S.I., summoning him to the agency’s headquarters, in Aabpara, a neighborhood in eastern Islamabad. When Shahzad showed up, he was met by three I.S.I. officers. The lead man, he said, was a naval officer, Rear Admiral Adnan Nazir, who serves as the head of the I.S.I.’s media division.

“They were very polite,” Shahzad told me. He glanced over his shoulder. “They don’t shout, they don’t threaten you. This is the way they operate. But they were very angry with me.” The I.S.I. officers asked him to write a second story, retracting the first. He refused.

And then Admiral Nazir made a remark so bizarre that Shahzad said he had thought about it every day since.

“We want the world to believe that Osama is dead,” Nazir said.

Bin Laden was still alive, his whereabouts presumably unknown, when that conversation occurred. I pressed Shahzad. What did they mean by that?

He shrugged and glanced over his shoulder again. They were obviously trying to protect bin Laden, he said.

“Do you think the I.S.I. was hiding bin Laden?” I asked him.

Shahzad shrugged again and said yes. But he hadn’t been able to prove it. (The I.S.I. calls this claim an “unsubstantiated accusation of a very serious nature.”)