Soon after the Navy SEAL raid on Bin Laden’s house, a Pakistani official told me that the United States had direct evidence that the ISI chief, Lt. Gen. Ahmed Shuja Pasha, knew of Bin Laden’s presence in Abbottabad. The information came from a senior United States official, and I guessed that the Americans had intercepted a phone call of Pasha’s or one about him in the days after the raid. “He knew of Osama’s whereabouts, yes,” the Pakistani official told me. The official was surprised to learn this and said the Americans were even more so. Pasha had been an energetic opponent of the Taliban and an open and cooperative counterpart for the Americans at the ISI. “Pasha was always their blue-eyed boy,” the official said. But in the weeks and months after the raid, Pasha and the ISI press office strenuously denied that they had any knowledge of Bin Laden’s presence in Abbottabad.

Colleagues at The Times began questioning officials in Washington about which high-ranking officials in Pakistan might also have been aware of Bin Laden’s whereabouts, but everyone suddenly clammed up. It was as if a decision had been made to contain the damage to the relationship between the two governments. “There’s no smoking gun,” officials in the Obama administration began to say.

The haul of handwritten notes, letters, computer files and other information collected from Bin Laden’s house during the raid suggested otherwise, however. It revealed regular correspondence between Bin Laden and a string of militant leaders who must have known he was living in Pakistan, including Hafiz Muhammad Saeed, the founder of Lashkar-e-Taiba, a pro-Kashmiri group that has also been active in Afghanistan, and Mullah Omar of the Taliban. Saeed and Omar are two of the ISI’s most important and loyal militant leaders. Both are protected by the agency. Both cooperate closely with it, restraining their followers from attacking the Pakistani state and coordinating with Pakistan’s greater strategic plans. Any correspondence the two men had with Bin Laden would probably have been known to their ISI handlers.