The millennium began with a hijacking of an Indian airliner to Kandahar, Afghanistan. The plot, involving the Pakistani terror group Harakat-ul-Mujahedin, al-Qaeda, the Afghan Taliban and Pakistan’s Inter-Services Intelligence Directorate (ISI), was a harbinger of a decade of terror whose epicenter was Pakistan—and this year the trail to high-value target number one, Osama bin Laden, finally ended there.

On a clear night in early May 2011, American Navy commandos found and killed Bin Laden in his hideout in the Pakistani city of Abbottabad. After searching since 1998, the Central Intelligence Agency had finally found the most wanted man in human history. Thorough and careful intelligence analysis had tracked him down to a house in the garrison city that also houses Pakistan’s premier military academy. Abbottabad is just thirty miles north of the country’s capital, Islamabad, and the nearby military-general headquarters in Rawalpindi. It is located on the famous Karakoram Highway, which follows the ancient Silk Road from South Asia over the Himalayas and Hindu Kush to China. In American terms, it was as if Bin Laden were hiding just outside the gate of the U.S. Naval Academy in Annapolis, Maryland, an hour’s drive from the White House and the Pentagon.

Abbottabad is named after a British army officer and colonial administrator, Sir James Abbott, who founded the city as a cantonment for the British army in India in January 1853. Abbott fought in the British East India Company’s wars against the Sikhs in the middle of the nineteenth century and was very fond of the city he founded.

The CIA traced Bin Laden there by following the trail of a Pakistani acting as his courier, Abu Ahmed al-Kuwaiti. Al-Kuwaiti had worked with Bin Laden in the planning of the 9/11 attacks and was his trusted emissary for carrying messages to the outside world. A Pakistani Pashtun tribesman who was born and raised in Kuwait and spoke fluent Arabic and Pashto, Al-Kuwaiti could move between two cultures easily. In 2010, the intelligence community traced him to Abbottabad and a three-story housing compound that seemed different from most other homes in the city. It was surrounded by an eighteen-foot-high wall topped with barbed wire, had no electronic signatures (phone or Internet), and seemed custom-built to hide someone. Privacy screens and interior walls obstructed vision into the compound from the outside. The children inside were home schooled, and the residents burned all of their garbage.

Bin Laden had apparently moved into the house sometime in 2006, the facility having been customized for him in 2005. He was a recluse inside but not isolated from the world. Al-Kuwaiti brought him messages and letters from the outside, and Bin Laden dispatched his letters via his courier. After his death, the SEAL commandos scooped up scores of documents and computer files. In those were found correspondence from Bin Laden to his wives, children, and subordinates such as Ayman al-Zawahiri and others. He was very much in charge of his global terrorist empire and kept abreast of plots like the July 2005 London bombing. He was constantly pressing his lieutenants for more terror.

Al-Qaeda practiced good tradecraft in concealing its leader’s hideout for five years. But he could not hide in Abbottabad without some support network beyond al-Kuwaiti. Phone numbers found in the house by the SEAL team suggest that al-Kuwaiti was in touch with a Pakistani terrorist group. As reported by the New York Times in June 2011, al-Kuwaiti was apparently in contact with the Harakat-ul-Mujahedeen terror group, the same group he had collaborated with a decade before in the millennium plot. It was created in the 1980s by ISI to fight India and has loyally worked with the Pakistani intelligence service for decades. Its leader is Fazlur Rehman Khalil, who lives openly in an Islamabad suburb.

The most important mystery, of course, is what the Pakistani army and the ISI knew about Bin Laden’s hideout. From the day the CIA became focused on Abbottabad, President Barack Obama decided that he could not trust the Pakistanis with information about the hideout. No Pakistani official was given any advance warning that the United States suspected Bin Laden was hiding in the Abbottabad complex or that Washington intended to send commandos to either capture or kill him. During months of surveillance of the compound and preparation for the SEAL operation, Pakistan was kept completely in the dark by Obama and his national-security team.

It was an extraordinary decision. Since 2001, Pakistani leaders from General and later President Pervez Musharraf to today’s President Ali Asif Zardari and the chief of army staff General Ashfaq Parvez Kayani, the real power in the country, had repeatedly promised to help America fight al-Qaeda. Now the American president correctly judged he could not trust them with vital information on the location of al-Qaeda’s top leader. Obama’s decision spoke volumes about America’s real attitude toward its Pakistani partner.

Abbottabad is not an ordinary city. Pakistan’s first military dictator, Field Marshall Ayub Khan, was born very close by. It is the home of the Kakul Military Academy, the Pakistani equivalent of West Point or Sandhurst. Some generals retire to its pleasant weather and surroundings. In short, from its founding during the Raj to today, it is a military city.

From the moment the SEAL raid became public, Pakistanis have wondered what their army and intelligence services knew about Bin Laden’s lair. One thing is certain—no one believes President Zardari knew anything about Bin Laden’s hideout. He is powerless and clueless about what the ISI is up to. Officially, the ISI says it too was clueless. Many Pakistanis find that hard to believe. Three days after the raid, an op-ed in the influential newspaper Dawn entitled “The Emperor’s Clothes” noted that “there is a deep, deep sense of unease here. Pakistanis are asking did the army know he was there? They knew. They knew he was there (in Abbottabad). And they knew they could get away with it.”

But we don’t really know. Perhaps the ISI really was ignorant of Bin Laden’s whereabouts and negligent in looking for him. Maybe Musharraf and Kayani were just incompetent. They had been warned to look in Abbottabad.

The Afghan intelligence chief, Amrullah Saleh, says he told Musharraf in 2006 in a meeting in Pakistan that Bin Laden was hiding in the area around Abbottabad. According to Saleh, in response to the news Musharraf “banged the table and said am I president of a banana republic? How can you tell me Bin Laden is hiding in a settled area of Pakistan?”

The question of negligence or complicity about the army’s role in Bin Laden’s hideout is much more than academic. It has grave policy implications. If the army was clueless about finding where al-Qaeda’s leader was hiding for at least half a decade, then we can not rely on it to fight terror effectively. If the inner circle of al-Qaeda’s core, sometimes called al-Qaeda al-Umm, or “mother al-Qaeda” in Arabic, could outfox the ISI so easily, then Pakistani intelligence is a very weak partner.

But if the army or parts of it were complicit in hiding Bin Laden for years, it suggests an astonishing degree of duplicity. A complicit army would have been al-Qaeda’s ally behind the scenes for years, maybe all the way back to 9/11. It would be the secret patron of global jihad on a scale almost too dangerous to conceive. We would need to rethink our entire relationship with Pakistan and our understanding of its strategic motives.

If only a part of the army, an errant general perhaps, were complicit, it raises serious questions about the army’s cohesion and internal loyalties. Who was the rogue, and who knew what he was up to? How many others are like him, perhaps guarding nuclear-weapons depots?

For now, we don’t know. The mystery of Abbottabad hangs like a black cloud over the future of U.S.-Pakistani relations. From that May night, the relationship has deteriorated quickly. American aid to Pakistan has been cut, clashes between NATO and Pakistani troops along the Afghan border have become deadly, the Zardari government is collapsing in a scandal called “memogate” that revolves around the question of the army’s complicity. Distrust on both sides is at an all time high.

Al-Qaeda al-Umm has been devastated by Bin Laden’s death and the drone war, but it is not yet defeated. If the pressure eases, it will grow back quickly. It still has many allies in Pakistan, including Harakat-ul-Mujahedin and others. The power of its allies in the army remains a mystery.

Bruce Riedel is a senior fellow in the Saban Center for Middle East Policy at the Brookings Institution. A career CIA officer, he has advised four presidents on Middle East and South Asian issues in the White House on the staff of the NSC. He is author of The Search for Al-Qaeda (Brookings Institution Press, 2008) and the forthcoming Deadly Embrace: Pakistan, America and the Future of the Global Jihad (Brookings Institution Press, 2011).

Image: U.S. Federal Government