In all three cases, Clarke sharply criticized the Bush administration's attitude toward counter-terrorism before the September 11 attacks, and its decision afterward to wage war and invade Iraq.

Years after Clarke left,[4] some components of the program were acquired by a sequence of firms, and it is reported they eventually surveilled women's rights activists, UN diplomats, and FIFA officials.

[6] After starting as a management intern at the U.S. Department of Defense and later working as an analyst on European security issues, Clarke went to graduate school.

Beginning in 1985, Clarke was appointed by the Ronald Reagan administration as Deputy Assistant Secretary of State for Intelligence—his first political appointee position as a Republican Party member.

Clarke continued as counter-terrorism coordinator at the NSC during the first year of the George W. Bush administration, but no longer had access, as the position's scope was reduced.

Timothy M. Carney, U.S. ambassador to Sudan between September 1995 and November 1997, co-authored an op-ed in 2002 claiming that in 1997, Sudan offered to turn over its intelligence on bin Laden to the US, but that Susan Rice, as National Security Council (NSC) Africa specialist, together with NSC terrorism specialist Richard A. Clarke, successfully lobbied for continuing to bar U.S. officials, including the CIA and FBI, from engaging with the Khartoum government.

[10] Similar allegations (that Susan Rice joined others in missing an opportunity to cooperate with Sudan on counter-terrorism) were made by David Rose, Vanity Fair contributing editor,[11] and Richard Miniter, author of Losing Bin Laden.

[12] Clarke was involved in supervising the investigation of Ramzi Yousef, one of the main perpetrators of the 1993 World Trade Center bombing, who had traveled to the United States on an Iraqi passport.

Many in the Clinton administration and the intelligence community believed Yousef's ties were evidence linking al-Qaeda's activities and the government of Iraq.

[13] In February 1999, Clarke wrote the Deputy National Security Advisor that a reliable source reported Iraqi officials had met with Bin Laden and may have offered him asylum.

Clarke advised against surveillance flights to track bin Laden in Afghanistan: he said that anticipating an attack, "old wily Usama will likely boogie to Baghdad," where he would be impossible to find.

Matthew Continetti wrote: Scheuer believes that Clarke's risk aversion and politicking negatively impacted the hunt for bin Laden prior to September 11, 2001.

Scheuer stated that his unit, codename "Alec," had provided information that could have led to the capture and or killing of Osama bin Laden on ten occasions during the Clinton administration, only to have his recommendations for action turned down by senior intelligence officials, including Clarke.

Despite severe criticism, Clarke and Sheehan prevailed upon President Clinton to resist international pressure and continue the US's solo veto.

The United States fought a four-round veto duel with France, forcing it to back down and accept the selection of US-educated Kofi Annan as the next Secretary-General.

[19] In his memoir, Against All Enemies, Clarke wrote that Condoleezza Rice decided that the position of National Coordinator for Counterterrorism should be downgraded.

No longer would Clarke's memos go to the President; instead they had to pass through a chain of command of National Security Advisor Condoleezza Rice and her deputy Stephen Hadley, who bounced every one of them back.

Rice told me that the Principals Committee, which had been the first venue for terrorism policy discussions in the Clinton administration, would not address the issue until it had been 'framed' by the Deputies.

Deputy Secretary of Defense Paul Wolfowitz responded, "Well, I just don't understand why we are beginning by talking about this one man bin Laden."

Clarke said that before and during the 9/11 crisis, many in the administration were distracted from taking action against Osama bin Laden's al-Qaeda organization because of an existing pre-occupation with Iraq and Saddam Hussein.

In response, Clarke wrote a report stating there was no evidence of Iraqi involvement: all relevant agencies, including the FBI and the CIA, signed off on this conclusion.

[26][27] Supporting Clarke's claim that intelligence forewarning of attacks had been delivered to the president prior to 9/11, former Deputy Attorney General Jamie Gorelick, the sole member of the 9/11 Commission permitted (under an agreement with the Bush administration) to read the President's Daily Brief, said that these had contained "an extraordinary spike" in intelligence warnings of al-Qaeda attacks that had "plateaued at a spike level for months" before 9/11.

Frist later speculated to reporters Clarke was trading on his former service as a government insider with access to the nation's most valuable intelligence to sell a book.

"[24] Another point of attack was Clarke's role in allowing members of the bin Laden family to fly to Saudi Arabia on September 20, 2001.

"[39] On March 28, 2004, at the height of the controversy during the 9/11 Commission Hearings, Clarke went on NBC's Sunday morning news show Meet the Press and was interviewed by journalist Tim Russert.

Clarke wrote an op-ed for The Washington Post, titled "The Trauma of 9/11 Is No Excuse" (May 31, 2009) harshly critical of other Bush administration officials.

In stemming cyber attacks carried out by foreign governments and foreign hackers, particularly from China, Clarke opined that the U.S. government should be authorized to "create a major program to grab stolen data leaving the country" in a fashion similar to how the U.S. Department of Homeland Security currently searches for child pornography that crosses America's "virtual borders."

"[45] In 2013, Clarke served on an advisory group for the Obama administration, as it sought to reform NSA spying programs following the revelations of documents released by Edward Snowden.

[48] As of August 2017, Clarke had been obtaining large amounts of funds, notably $20 million for the Middle East Institute via the Emirates Center for Strategic Studies and Research (ECSSR), an Abu Dhabi-based think tank.

The Intercept reported that Saif Mohamed Al Hajeri, CEO of Tawazun Holding L.L.C., had been sanctioning the money, larger than the annual budget of the Middle East Institute, on orders of Otaiba.