Besides branches specializing in Lebanon's Hezbollah, and secular groups like the Japanese Red Army, another concentrated on Sunni Islamist radicalism, primarily in Algeria.

[5] Former CTC Director Cofer Black illustrates the evolution of the organization's priorities throughout the 1990s during the 9/11 commission, explaining:During the early and mid-1990's, al-Qa'ida was not our principal counterterrorism target.

[9] Early in 1999, Tenet ordered the CTC to conduct a review of the CIA's operational strategy to create "a new, comprehensive plan of attack" against al-Qaeda.

[citation needed] By mid-September, the result of this review, known simply as "The Plan", had been briefed to CIA operational level personnel and the NSA, the FBI, and other partners.

[10] Beginning in September 1999, the CTC picked up multiple signs that bin Laden had set in motion major terrorist attacks for the turn of the year.

[11] Amid this activity, in November–December 1999, Mohamed Atta, Marwan al-Shehhi, Ziad Jarrah, and Nawaf al-Hazmi visited Afghanistan, where al-Qaeda selected them for the 9/11 operation.

[12] In late 1999, the NSA picked up traces of an "operational cadre" consisting of al-Hazmi, his younger brother Salem, and Khalid al-Mihdhar, who were planning to go to Kuala Lumpur, Malaysia, in January 2000.

[13] At about this time, the SOCOM-DIA data mining operation "Able Danger" also identified a potential al-Qaeda unit, consisting of the future leading 9/11 hijackers, and termed them the "Brooklyn cell".

[16][17] In autumn 2000, a series of flights over Afghanistan by Predator drones, under the joint control of the U.S. Air Force and the CTC, produced probable sightings of bin Laden.

CTC Director Black advocated arming Predators with missiles to try to launch a targeted killing of bin Laden, but there were legal and technical issues.

On Black's advice, Director George Tenet raised the matter at the long-awaited Cabinet-level Principals Committee meeting on terrorism on September 4, 2001, and received authorization to deploy the system.

After the September 11, 2001 attacks on the United States, some CTC staff were exempted from an order to evacuate the CIA headquarters building at Langley.

[18] The CTC obtained passenger lists from the planes used in the attack and identified Khalid al-Mihdhar and Nawaf al-Hazmi,[19] whose names they had first linked with terrorism in the winter of 1999–2000.

Execution of this mission was nowhere more evident than at Qala-i-Jangi, a 19th-century fortress on the outskirts of the northern Afghan town of Mazar-i-Sharif, when it fell to American allies.

In addition to creating the first new directorate for the agency in nearly fifty years, many changes surrounded the creation of 10 new "mission centers" modeled on CTC, which combine analysts and operators in hybrid units focused on specific regions or security threats.

[28] Long seen as redundancy by some in departments of the constituent agencies of the Intelligence Community for having a similar and sometimes overlapping mission with what they see as the territory better left to their units like CTMC, the Trump administration's more significant move to downsize NCTC was less surprising to most than the abrupt dismissal.