On the morning of 11 September 2001, nineteen al-Qa’ida terrorists hijacked four commercial airliners. Two slammed into the north and south towers of lower Manhattan's World Trade Center complex, causing the twin towers to crumble; one plane smashed into the Pentagon in Arlington, Virginia; and one crashed in a field in Shanksville, Pennsylvania, after passengers heroically fought back against the hijackers. Nearly 3,000 people, from many countries, were killed that morning after eighteen Saudi Arabian citizens and one Lebanese, having identified security weaknesses in America’s civil aviation sector, caused ten billion dollars’ worth of property damage and changed the course of history. The reverberations of the attacks and the international response to them are still felt today.

CIA headquarters itself was evacuated due to the fear that it might have been the target of one of the hijacked airliners. For those who worked counterterrorism accounts in the American intelligence community there was no need to wait for claims of responsibility; several of them stayed at their desks in Langley to keep information flowing despite the general evacuation order. The attack had all the hallmarks of al-Qa’ ida – a spectacular simultaneous mass casualty event on a symbolic target, echoing both the 1993 World Trade Center attack and also 1998 twin East Africa embassy bombings on a much larger scale.

As CIA's analytical cadre worked overtime to unravel details of the plot, its paramilitary Special Activities Division (SAD) began recontacting sources from the 1980s, when they had fought together against the Soviet invasion of Afghanistan. A few weeks after 9/11, CIA's paramilitary ‘Jawbreaker’ team was on the ground and ready to aid the primary resistance to the Taliban regime in Afghanistan, a loosely coordinated coalition generally known as the Northern Alliance. CIA set to work with US military Special Forces troops to dismantle al-Qa’ida’s support structure and training camps. This was dangerous work; very few Americans were on the ground in Afghanistan during the early phase of the operation, and some of those that were had been literally pulled out of the retirement process.

In late November, CIA suffered its first post-9/ 11 casualty when paramilitary officer Johnny ‘Mike’ Spann was killed during a prisoner uprising at the Qala-i-Jangi prison near Mazar-i-Sharif, Afghanistan. Spann, a former Marine captain, was interrogating prisoners and attempting to discover bin Ladin's whereabouts.