Shahzad, 40, vanished on May 29 after writing about alleged links between Al-Qaeda and the Pakistani Navy. His body was found on May 31 in a canal near the town of Mandi Bahauddin, about 75 miles (120 kilometers) south of the capital, Islamabad. His friends said the body showed signs of torture around the face and neck. He had told colleagues that he had been receiving threats from intelligence officials in recent months.

Shahzad was reported missing after he failed to show up for a televised panel discussion in Islamabad. He was scheduled to discuss his recent article for Asia Times Online in which he reported that Al-Qaeda, having infiltrated the Pakistani Navy, was behind a 17-hour siege at a naval base in Karachi on May 22. He said the attack came after military or security officials refused to release a group of naval officials suspected of being linked to militant groups. The attack, coming soon after the U.S. killing of Osama bin Laden on May 2, was deeply embarrassing to the Pakistani military. Earlier in May, three navy buses carrying recruits were blown up via remote control devices in Karachi, the large port city where the navy has its headquarters.

Shahzad's death also came a few days after the release of his book, Inside the Taliban and Al-Qaeda.

For months, the journalist had been telling friends that he had been warned by intelligence agents to stop reporting on sensitive security matters. In October 2010, Shahzad told Ali Dayan Hasan, a researcher for Human Rights Watch in Pakistan, that he had been threatened by a top official at a meeting at the headquarters of the Inter-Services Intelligence Directorate in Rawalpindi.

Hasan said Shahzad sent him a note describing the meeting "in case something happens to me or my family in the future," Human Rights Watch reported. Hameed Haroon, president of the All Pakistan Newspapers Society and a former employer of Shahzad, said he had received a similar message at about the same time.

In July 2011, The New York Times reported that U.S. officials had reliable intelligence that showed that the ISI was responsible for Shahzad's murder. Pakistan's official commission of inquiry concluded in January 2012 that the perpetrators were unknown, a finding that was widely criticized as lacking credibility.