Richard Clarke, 9/11, and the Continuity of Government Plan
The morning of 9/11, a highly secret plan was activated for the first time. Called continuity of government (COG), it dated back to the cold war and had originally been designed to ensure the U.S. government would continue to function in the event of a nuclear war. According to author James Mann, this little-known plan "helps to explain the thinking and behavior" of the Bush administration, "in the hours, days, and months after the terrorist attacks on September 11, 2001." 
Donald Rumsfeld and Dick Cheney, who on 9/11 were the secretary of defense and vice president, were key players in the COG program throughout the 1980s. Both regularly participated in secret exercises rehearsing the plan. Furthermore, a third Bush administration official was also a major player. That person was Richard Clarke, who on September 11 was the White House chief of counterterrorism. Not only was he a regular participant in the COG exercises, Clarke also wrote a presidential directive that in 1998 changed the focus of the program from the Soviet threat to the threat posed by terrorists. And, according to his own recollection, it was Clarke that initiated COG on the morning of 9/11. This means that on September 11, individuals in three of the most important positions within the U.S. government, who all had crucial roles to play during the attacks, had in common their participation in this most secretive and mysterious program.
RICHARD CLARKE ON 9/11
In his book Against All Enemies, Richard Clarke described how he personally ordered the COG plan into effect during the 9/11 attacks. At around 9:45-9:55 that morning, he had been joined in the White House Situation Room by the coordinator for continuity of government. Clarke asked him, "How do I activate COG?" According to Clarke, "In the exercises we had done, the person playing the president had always given that order." But the coordinator replied, "You tell me to do it." Clarke ordered him, "Go." 
If this account is accurate, then Clarke's central role in COG becomes obvious: He was able to initiate the plan, performing a task conducted by the acting president during exercises.
Clarke has explained what happened next: "Every federal agency was ordered ... to activate an alternative command post, an alternative headquarters outside of Washington, DC, and to staff it as soon as possible." Cabinet officers were dispatched around the U.S., and members of Congress were taken to alternative locations. According to ABC News, "If executive branch leaders and large numbers of congressmen had been killed ... the plan could have gone further, officials suggest, perhaps even with non-elected leaders of the United States taking control and declaring martial law." 
RICHARD CLARKE PARTICIPATES IN COG EXERCISES
In 2004, Clarke revealed that over the previous 20 years he had been a regular participant in exercises where he had "gone off into caves in mountains in remote locations and spent days on end in miserable conditions, pretending that the rest of the world had blown up."  As part of a program with a secret budget of hundreds of millions of dollars per year, these exercises rehearsed the COG plan. During the 1980s, teams of 40 to 60 federal officials, plus a member of President Reagan's Cabinet, would disappear at least once a year to a remote location such as an underground bunker or a disused military base. There they would practice in detail how to keep the federal government running during and after a nuclear war with the Soviet Union. Donald Rumsfeld and Dick Cheney were also among those who regularly participated in these exercises. 
Despite the fall of the Soviet Union, the exercises continued throughout the 1990s and the program's budget remained at over $200 million a year. But now the exercises practiced for the threat posed by terrorists. 
PDD-67: TERRORISM BECOMES THE NEW THREAT
In early 1998, while he was the chair of the White House's Counterterrorism Security Group (CSG), Richard Clarke wrote the Presidential Decision Directive (PDD) that updated the COG program to make its focus terrorism rather than the Soviet Union. As he later explained: "We thought that individual buildings in Washington, and indeed perhaps all of Washington, could still come under attack, only it might not be from the former Soviet Union. ... It might be with a terrorist walking a weapon into our city."  Clarke has recalled, "If terrorists could attack Washington, particularly with weapons of mass destruction, we needed to have a robust system of command and control, with plans to devolve authority and capabilities to officials outside Washington." President Clinton signed Clarke's directive on October 21, 1998, as Presidential Decision Directive 67, "Enduring Constitutional Government and Continuity of Government Operations." 
This top-secret document has never been released, and there is no White House fact sheet summarizing its contents.  But Knight Ridder reported in 1999 that PDD-67 required "agencies to prepare plans for governmental continuity if the country is hit by a major terrorist attack." According to Energy Department emergency planning documents, the continuity plans "could be triggered by an event worse than what's expected from the Y2K problem and comparable to the 1995 Oklahoma City bombing."  The Washington Post reported that, under PDD-67: "[E]very single government department and agency was directed to see to it that they could resume critical functions within 12 hours of a warning, and keep their operations running at emergency facilities for up to 30 days. FEMA [the Federal Emergency Management Agency] was put in charge of this broad new program."  The fact that he wrote such a key document again shows the central role Clarke must have had within the COG program. And, as it could be triggered "by an event ... comparable to the 1995 Oklahoma City bombing," it appears that Clarke's directive may be what enabled COG to be activated in response to the 9/11 attacks.
In light of his involvement with the continuity of government program, it is worth noting that, while he has become well known for his criticisms of the Bush administration's pre-9/11 failures, Richard Clarke is by no means a peace-loving liberal. Some who have known him have in fact described quite the opposite. According to the Washington Post, many in the Clinton administration viewed him as a hawk.  Robert Gelbard, who worked with him at the State Department in the early 1990s, said Clarke is "no liberal. He is very hawkish."  Larry DiCara, the former president of the Boston City Council, who knew Clarke when he was younger, has described him as "fiercely conservative at a time when just about everyone in Boston was a Democrat." DiCara added, "I'm amazed he worked for [President] Clinton." 
As early as February 1999, Clarke was articulating the desire for a particularly aggressive foreign policy, telling the Associated Press: "We may not just go in a strike against a terrorist facility. We may choose to retaliate against the facilities of the host country, if that host country is a knowing, cooperative sanctuary."  In April 2000, he told the Washington Post: "We should have a very low barrier in terms of acting when there is a threat of weapons of mass destruction being used against American citizens. We should not have a barrier of evidence that can be used in a court of law."  That year, The Independent called Clarke "the Dr. Strangelove de nos jours," while The Spectator magazine later described him as having "frequently sounded more Bush-like than Bush," prior to his much-publicized attacks on the president in 2004. 
Indeed, according to journalist and author Andrew Cockburn, during the 1990s, the COG exercises Clarke participated in were attended "almost exclusively" by Republican hawks. A former Pentagon official with direct knowledge has described: "It was one way for these people to stay in touch. They'd meet, do the exercise, but also sit around and castigate the Clinton administration in the most extreme way. You could say this was a secret government-in-waiting. The Clinton administration was extraordinarily inattentive, [they had] no idea what was going on." 
 James Mann, "The Armageddon Plan." Atlantic Monthly, March 2004.
 Richard Clarke, Against All Enemies: Inside America's War on Terror. New York: Free Press, 2004, p. 8.
 "Worst Case Scenario: Secret Plan to Control U.S. Government After an Attack Went Into Motion on 9/11." ABC News, April 25, 2004.
 Howard Kurtz, "'Armageddon' Plan Was Put Into Action on 9/11, Clarke Says." Washington Post, April 7, 2004.
 James Mann, "The Armageddon Plan."
 Andrew Cockburn, Rumsfeld: His Rise, Fall, and Catastrophic Legacy. New York: Scribner, 2007, p. 88.
 CBS News, September 11, 2001.
 Richard Clarke, Against All Enemies, pp. 167 and 170; William M. Arkin, "Back to the Bunker." Washington Post, June 4, 2006.
 "PDD-NSC-67: Enduring Constitutional Government and Continuity of Government Operations (U) 21 October 1998." Federation of American Scientists, December 12, 2000.
 Jim Landers, "Government Uses Y2K Lessons in its Blueprint for Cyber-Terror Defenses." Knight Ridder, November 17, 1999.
 William M. Arkin, "Back to the Bunker."
 Dan Eggen and Walter Pincus, "The Book on Richard Clarke." Washington Post, March 23, 2004.
 David E. Kaplan, "Clarke: A Man on a Mission." U.S. News & World Report, April 5, 2004.
 David Abel, "Conservative Side Showed in Hub Days." Boston Globe, March 29, 2004.
 "USA Claims Right to Bomb Kabul." Associated Press, February 8, 1999.
 Michael Dobbs, "An Obscure Chief in U.S. War on Terror." Washington Post, April 2, 2000.
 Andrew Marshall, "Losing the War for Justice Against the 'Islamic Menace.'" The Independent, August 23, 2000; Mark Steyn, "Murderous Rhetoric." The Spectator, April 10, 2004.
 Andrew Cockburn, Rumsfeld, p. 88.