On Sept. 11, 2001, the core of al-Qaeda was concentrated in a single city: Karachi, Pakistan. At a hospital, the accused mastermind of the bombing of the USS Cole was recovering from a tonsillectomy. Nearby, the alleged organizer of the 2002 bombing in Bali, Indonesia, was buying lab equipment for a biological weapons program. And in a safe house, the man who would later describe himself as the intellectual author of the Sept. 11 attacks was with other key al-Qaeda members watching the scenes from New York and Washington unfold on television.