It took America’s Central Intelligence Agency 15 long years to finally catch up with the guy who sparked the biggest manhunt in its history.

And its tall, lanky target was not found in the “hole” from which former US President George W. Bush had pledged to smoke him out. It turned out he had been living a stone’s throw from Pakistan’s main military academy in Abbotabad.

For several years before the American raid that killed Osama bin Laden on May 2, his trail had gone cold. He had disappeared from Tora Bora in Afghanistan’s eastern Nangarhar province in the winter of 2001, just when the United States believed it had boxed in the 9/11 mastermind along with hundreds of his loyalists. Little was known about his whereabouts after he was last overheard giving commands over a shortwave radio.

It was in South Waziristan, according to intelligence officials, that the fugitive began his long journey in Pakistan, staying one night in one place and relocating to another the next. Unlike his lieutenant, the bespectacled Dr Ayman al-Zawahiri, who did most of the legwork of running Al Qaeda and was sighted in Pakistan’s tribal regions several times, he managed to remain unnoticed. Communication intercepts and human intelligence failed to pinpoint the location of the man whose head carried a $50m bounty, but he was generally believed to be in Pakistan’s tribal areas. One video that showed bin Laden walking alongside Zawahiri in a mountainous region instead drew the attention of intelligence analysts to Pakistan’s Chitral and Afghanistan’s Nuristan provinces due to their topographies, but couldn’t lead to his capture. Meanwhile, speculations surrounding his health on account of kidney problems and hypertension continued to do the rounds. Many thought he was likely to have died.

While conventional wisdom assumed he would be maintaining several go-betweens and a large security detail, the Al Qaeda chief later turned out to have kept just two guards at the Abbottabad compound who were brothers from Malakand and whose father had worked in the bin Laden family’s construction firm in Saudi Arabia. One of them served as a courier, helping him evade capture. To avoid outside contact he grew his own vegetables, raised his own poultry and had one of his wives home-school his children and grandchildren.

The first indication that bin Laden could still be around emerged with the arrest of the Indonesian mastermind of the 2002 Bali bombing, Umar Patek, in Abbottabad in January. The head of Indonesia’s National Counter-Terrorism Agency claimed Patek was there to discuss new attacks with the Al Qaeda leader to coincide with the tenth anniversary of 9/11.

This was followed by a telephone intercept of one of the two guards that indicated what region bin Laden might be in, information that Pakistani intelligence shared with their American counterparts. Officials now say that while the Americans had played down the significance of that critical bit of intelligence at the time, the CIA followed up on it, monitoring occasional intercepts and eventually homing in spy satellites on the compound in Abbottabad where OBL would later be found.

The Pakistanis took a back seat. Inter-Services Intelligence and the CIA worked in tandem and shared intelligence, but their goals were different. For the ISI, the Tehrik-i-Taliban Pakistan was the bigger priority.

Meanwhile, the CIA recruited a Pakistani doctor and organised a fake vaccination program to peep into bin Laden’s compound. The route adopted by the American helicopter on May 2 to drop Navy Seals into the compound was surveyed beforehand and, unbeknown to Pakistani officials, a refuelling spot was set up in the remote Kala Dhaka area of Mansehra district. If the Pakistani military and government are to be believed, the raid took both Rawalpindi and Islamabad by surprise.

Inevitably for a project shrouded in such mystery, the CIA’s Operation Neptune Spear raised more questions than it answered. The speed with which bin Laden’s body was disposed of at sea caused speculation about the reality of his presence in the Abbottabad compound. But blood samples collected by Pakistani investigators from the spot matched the DNA of his children, and his family members found at the scene confirmed he had been there.

The broader, louder questions that emerged were about the future of the tenuous US-Pakistan relationship. Stuck with a new embarrassment just a few months after the Raymond Davis incident, Islamabad ordered an investigation whose outcome is still pending. But that did not prevent concern on both sides about the level of trust between the two so-called partners and their spy agencies. In America’s eyes, public enemy number one had been recovered from the soil of a supposed ally. In Pakistan’s eyes, an ally had violated its sovereignty. It is not a setback the relationship has recovered from.

— Ismail Khan is Dawn’s resident editor in Peshawar