The two young visitors who stopped for a night at the madrasa were escorted the next day to Rawalpindi, where Bhutto would be speaking at a rally on Dec. 27. As her motorcade left the rally, it slowed so she could greet supporters in the street. One of the two teenagers fired a pistol at her and then detonated his vest of explosives. Bhutto was standing in the roof opening of an armored S.U.V. She ducked into the vehicle at the sound of the gunfire, but the explosion threw the S.U.V. forward, slamming the edge of the roof hatch into the back of her head with lethal force. Bhutto slumped down into the vehicle, mortally wounded, and fell into the lap of her confidante and constant chaperone, Naheed Khan.

As Bhutto had long warned, a conglomeration of opponents wanted her dead and were all linked in some way. They were the same forces behind the insurgency in Afghanistan: Taliban and Pakistani militant groups and Al Qaeda, as well as the Pakistani military establishment, which included the top generals, Musharraf and Kayani. A United Nations Commission of Inquiry into the circumstances of Bhutto’s death found that each group had a motive and merited investigation.

Pakistani prosecutors later indicted Musharraf on charges of being part of a wider conspiracy to remove Bhutto from the political scene. There was “overwhelming circumstantial evidence” that he did not provide her with adequate security because he wanted to ensure her death in an inevitable assassination attempt, the chief state prosecutor in her murder trial, Chaudhry Zulfiqar Ali, told me. (Musharraf denied the accusations.) A hard-working, hard-charging man, Ali succeeded in having Musharraf arrested and was pushing to speed up the trial when he was shot to death on his way to work in May 2013.

Ali had no doubts that the mastermind of the plot to kill Bhutto was Al Qaeda. “It was because she was pro-American, because she was a strong leader and a nationalist,” he told me. A Pakistani security official who interviewed some of the suspects in the Bhutto case and other militants detained in Pakistan’s prisons came to the same conclusion. The decision to assassinate Bhutto was made at a meeting of the top council of Al Qaeda, the official said.

It took more than three years before the depth of Pakistan’s relationship with Al Qaeda was thrust into the open and the world learned where Bin Laden had been hiding, just a few hundred yards from Pakistan’s top military academy. In May 2011, I drove with a Pakistani colleague down a road in Abbottabad until we were stopped by the Pakistani military. We left our car and walked down a side street, past several walled houses and then along a dirt path until there it was: Osama bin Laden’s house, a three-story concrete building, mostly concealed behind concrete walls as high as 18 feet, topped with rusting strands of barbed wire. This was where Bin Laden hid for nearly six years, and where, 30 hours earlier, Navy SEAL commandos shot him dead in a top-floor bedroom.

After a decade of reporting in Afghanistan and Pakistan and tracking Bin Laden, I was fascinated to see where and how he hid. He had dispensed with the large entourage that surrounded him in Afghanistan. For nearly eight years, he relied on just two trusted Pakistanis, whom American investigators described as a courier and his brother.

People knew that the house was strange, and one local rumor had it that it was a place where wounded Taliban from Waziristan recuperated. I was told this by Musharraf’s former civilian intelligence chief, who had himself been accused of having a hand in hiding Bin Laden in Abbottabad. He denied any involvement, but he did not absolve local intelligence agents, who would have checked the house. All over the country, Pakistan’s various intelligence agencies — the ISI, the Intelligence Bureau and Military Intelligence — keep safe houses for undercover operations. They use residential houses, often in quiet, secure neighborhoods, where they lodge people for interrogation or simply enforced seclusion. Detainees have been questioned by American interrogators in such places and sometimes held for months. Leaders of banned militant groups are often placed in protective custody in this way. Others, including Taliban leaders who took refuge in Pakistan after their fall in Afghanistan in 2001, lived under a looser arrangement, with their own guards but also known to their Pakistani handlers, former Pakistani officials told me. Because of Pakistan’s long practice of covertly supporting militant groups, police officers — who have been warned off or even demoted for getting in the way of ISI operations — have learned to leave such safe houses alone.