The Counterterrorism Center (CTC) was a Central Intelligence Agency organization, unusual for the days before the 9-11 attack in that it mixed personnel from the operations and analytical directorates, as well from the Federal Bureau of Investigation. It had both intelligence and operational functions, although the "special operations" suffix was classified for some time. Established by Director of Central Intelligence (DCI) William Casey in 1986, it has been replaced by the National Counterterrorism Center (NCTC) in the Office of the Director of National Intelligence.
Under Casey, a fervent anticommunist, there was an assumption that worldwide terrorist groups were Soviet proxies. Casey received a proposal from Dewey Clarridge, a senior officer in the Directorate of Operations, to build a group that looked at terrorism on a global basis. Most of the Operations Division was then built around geographic divisions.
Paul Pillar became chief of analysis at the Agency's Counterterrorism Center (CTC) in 1993. By 1997 he was the Center's deputy director.
Threats change to Jihadists
Between 1999 and 2002, it was headed by Cofer Black. Pillar clashed with Black, took a leave as a Federal Executive Fellow at the Brookings Institution from 1999-2000,  and then permanently left the CTC.
In October 2001, Rolf Mowatt-Larsen was recruited by Director of Central Intelligence George Tenet to take on the understaffed and extremely sensitive weapons of mass destruction group within the CTC. In their first conversation, Black challenged Mowatt-Larsen that the classical noncoercive interrogation methods would not work with al-Qaeda members, and torture was specifically discussed. 
Afghanistan paramilitary operations
Hank Crumpton was the headquarters chief of the Afghanistan campaign from 2001 to 2002.
For some time, the suffix "Special Operations", in CTC/SO, was classified. The SO function directed CIA field activities in the Afghanistan War (2001-); the suffix was redacted from Gary Berntsen's book but allowed in Gary Schroen's. 
- J. Cofer Black (April 13, 2004), Testimony, National Commission on Terrorist Attacks Upon the United States
- Members: Paul Pillar, Council on Global Terrorism
- Steve Coll, Ghost Wars: The Secret History of the CIA, Afghanistan and Bin Laden, From the Soviet Invasion to September 10, 2001 (Penguin, 2005 revised edition), pp. 257, 375, 451, 457.
- Ron Suskind (2006), The One Percent Doctrine: Deep Inside America's Pursuit of its Enemies Since 9/11, Simon and Schuster, ISBN 9780743271097, pp. 49-53
- Gary Bertsen and Ralph Pezzulo (2005), JAWBREAKER: The attack on Bin Laden and al-Qaeda: A Personal Account by the CIA's Field Commander, Three Rivers Press, Crown Publishing Group, Random House, ISBN 0307351068, pp. 90-92
- Gary C. Schroen (2005), First In: An Insider's Account of How the CIA Spearheaded the War on Terror in Afghanistan, Ballentine, ISBN 0891418723