Mohammed Atef was the actual number three in al-Qaeda’s leadership — a position the CIA, in part because of confusion between two unrelated individuals using the kunya Abu Zubaydah, would later misattribute to Abu Zubaydah. Per John Kiriakou: “The actual number three was Mohammed Atef. But we killed Mohammed Atef in October of 2001 in Tora Bora. As soon as we started hitting Tora Bora, we hit the house that Mohammed Atef was in, and it turned out that when the rocket came through the roof it blew up the kitchen table, and a shard of wood from the table hit him in the neck and killed him.”[1][2] In a separate retelling, Kiriakou describes Atef taking cover under the kitchen table during the strike, with a splinter from the shattered table piercing his heart rather than his neck.[3]
How he died
Atef held al-Qaeda’s third position until October, when the CIA bombed the house he was hiding in at Tora Bora. Kiriakou’s account of the manner of his death is specific: the blast splintered the dining room table, and a chunk of wood went through his neck and killed him.[4] The vacancy that left is why the CIA was prepared to believe that Abu Zubaydah, taken the following spring, was the new number three — an inference Kiriakou notes would have made him only a few months old in the job, and therefore no use as a source on the planning of the September 11 attacks.[4][5]
Killed, where Zubaydah was taken
Kiriakou uses Atef as the marker for what was new about the Abu Zubaydah raid. “We had killed Mohammed Atef, who had been the director of military affairs for al-Qaeda. We were able to drone him to death in Tora Bora. But Abu Zubaydah was the first one we took alive” — and the first high-value target the agency had been able to locate and find at all.[6]
What he attaches to it is personal rather than operational: “catching him that night literally changed the course of the rest of my life. My life was never the same. For better, for worse — mostly for worse.”[7]