Al-Qaeda leader Hassan Ghul is secretly transferred from US custody to Pakistani custody. The Pakistani government will later release him and he will apparently rejoin al-Qaeda. In early 2004, Ghul was captured in Iraq and put in the CIA’s secret prison system (see January 23, 2004). He became a “ghost detainee” because the US refused to admit they even held him. In 2006, the Bush administration decides to close most of the CIA’s secret prisons and transfer most of the important al-Qaeda prisoners to the Guantanamo prison. But Ghul is given to the Pakistani government instead, apparently as a goodwill gesture. According to a 2011 article by the Associated Press, “[T]he move frustrated and angered former CIA officers, who at the time believed Ghul should have been moved to Guantanamo along with 14 other high-value detainees” (See September 2-3, 2006). The ISI, Pakistan’s intelligence agency, promises that it will make sure Ghul is never released. But after only about a year, Pakistan will secretly let Ghul go and he apparently will return to working with al-Qaeda (see (Mid-2007)). [Associated Press, 6/15/2011] Ghul is given to Pakistan even though he is linked to a Pakistani militant group supported by the ISI, Pakistan’s intelligence agency, and the ISI had a history of protecting him from arrest (see (2002-January 23, 2004)). Also, Ghul is released even though he told US interrogators key information about Osama bin Laden’s courier that will eventually prove key to the discovery of bin Laden’s location (see Shortly After January 23, 2004 and Late 2005).
Between July 28 and August 9, 2006: CIA Official Travels to Pakistan to Order Arrest of Liquid Bomb Suspect
Jose Rodriguez, head of the National Clandestine Service at the CIA, travels to Pakistan to order local authorities there to arrest a militant named Rashid Rauf. Rauf is currently in Pakistan, but is a key figure in a British-based conspiracy to blow up several airliners with liquid bombs (see August 10, 2006). The British had briefed US officials on the surveillance of the plotters, but the US had pushed for immediate arrests, whereas Britain wanted to monitor the men for longer to gather evidence for a later prosecution (see Before August 10, 2006). After the Pakistani authorities follow Rodriguez’s instruction to arrest Rauf—without the British being notified in advance—the British have no choice but to prematurely arrest the other plotters, as they fear they will learn of Rauf’s arrest and begin to destroy evidence and disperse. According to the London Times, Rodriguez is ordered to Pakistan by US Vice President Dick Cheney. Michael Clarke, director of the British Royal United Services Institute, will say that after British Prime Minister Tony Blair briefed President Bush on July 28: “Vice President Cheney despatched a man called Jose Rodriguez to Pakistan in secret.… And after Mr Rodriguez’s arrival in Pakistan, Rashid Rauf was picked up. The British were hopping mad about that, because it meant that on August 10 they had no choice but to move in on this plot before all the evidence was as mature as possible. There is a general belief in British security circles that the despatch of Mr Rodriguez to [Pakistan] came straight from the White House.” Based on Clarke’s assessment and other sources, including Andy Hayman, former assistant commissioner for specialist operations in the Metropolitan Police, the Times will conclude that Cheney “nearly destroyed Britain’s efforts to bring the airline bomb plotters to justice.” [Times (London), 9/8/2009]
Autumn 2006: Key Link between Al-Qaeda Leaders and Al-Qaeda in Iraq Is Arrested
Abd al-Hadi al-Iraqi, said to be an adviser to Osama bin Laden, is captured and detained in a secret CIA prison. President Bush announced on September 6, 2006 that the secret CIA prisons have just been emptied, at least temporarily (see September 2-3, 2006 and September 6, 2006). Nonetheless, Al-Hadi is put in the CIA’s secret prison system (see Autumn 2006-Late April 2007). Very little is known about al-Hadi’s arrest, which will not even be announced until late April 2007, shortly after he is transferred to the Guantanamo prison. It is unknown whether he is captured before Bush’s announcement (in which case he should have been sent to Guantanamo with other high-ranking prisoners), or after. [Salon, 5/22/2007] Prior to Al-Hadi’s arrest, the US government had posted a $1 million reward for his capture. His reward announcement calls him “one of Osama bin Laden’s top global deputies, personally chosen by bin Laden to monitor al-Qaeda operations in Iraq.… He has been associated with numerous attacks in Afghanistan and Pakistan and has been known to facilitate communication between al-Qaeda in Iraq and al-Qaeda.” The announcement notes that al-Hadi once served as a major in the Iraqi army, and he may still be in contact with bin Laden. [Rewards for Justice, 1/4/2007] In 2005, Newsweek reported that al-Hadi had been the main liaison between bin Laden and the independent minded Islamist militant leader Abu Musab al-Zarqawi in Iraq. [Newsweek, 4/4/2005]
Autumn 2006- February 2007: Head of US Forces in Afghanistan Compiles Dossier Showing Pakistan’s Support for Militants, but to Little Effect
In autumn 2006, President Bush declares in a White House news conference that al-Qaeda is “on the run,” but in fact intelligence reports are indicating that al-Qaeda is gaining strength in its safe haven in Pakistan’s tribal region. The New York Times will later comment, “with senior Bush administration officials consumed for much of that year with the spiraling violence in Iraq, the al-Qaeda threat in Pakistan was not at the top of the White House agenda.” Frustrated, Lt. Gen. Karl Eikenberry, the top US commander in Afghanistan, orders military officers, CIA, and US special forces to assemble a dossier documenting the Pakistani government’s role in allowing militants to establish their safe haven in the tribal region. According to the Times, “Behind the general’s order was a broader feeling of outrage within the military—at a terrorist war that had been outsourced to an unreliable ally, and at the grim fact that America’s most deadly enemy had become stronger.” When Eikenberry finally presents his dossier to several members of Bush’s cabinet, some inside the State Department and the CIA dismiss his warning as exaggerated and simplistic. [New York Times, 6/30/2008] On February 13, 2007, Eikenberry states publicly before a Congressional committee that NATO cannot win in Afghanistan without addressing the safe haven across the border in Pakistan. He does not publicly discuss Pakistan’s support for the militants, but he does say, “A steady, direct attack against the command and control in Pakistan in sanctuary areas is essential for us to achieve success.” He also warns that the US is facing a “reconstituted enemy” and “growing narcotics trafficking” in Afghanistan, which could lead to “the loss of legitimacy” of the government there. Eikenberry is already due to be replaced as commander of US forces in Afghanistan by the time he makes these blunt comments. [Washington Post, 2/14/2007; Rashid, 2008, pp. 383] The White House responds by sending Vice President Dick Cheney and CIA Deputy Director Stephen Kappes to Islamabad, Pakistan, later in February (see February 26, 2007). But there is little apparent change in Pakistan’s behavior. [New York Times, 6/30/2008]
September 2-3, 2006: US Temporarily Closes Secret CIA Prisons, Transfers Top Suspects to Guantanamo for Military Tribunals
The US temporarily closes a network of secret CIA prisons around the world and transfers the most valuable prisoners to the US prison in Guantanamo, Cuba, for eventual military tribunals. The prison network will be reopened a short time later (see Autumn 2006-Late April 2007). There were reportedly fewer than 100 suspects in the CIA prisons; most of them are apparently sent back to their home countries while fourteen are sent to Guantanamo. All fourteen have some connection to al-Qaeda. Seven of them reportedly had some connection to the 9/11 attacks. Here are their names, nationalities, and the allegations against them. 
Khalid Shaikh Mohammed (KSM) (Pakistani, raised in Kuwait). He is the suspected mastermind of 9/11 attacks and many other al-Qaeda attacks. A CIA biography of KSM calls him “one of history’s most infamous terrorists.” Mustafa Ahmed al-Hawsawi (Saudi). He allegedly helped finance the 9/11 attacks. Hambali (Indonesian). He attended a key planning meeting for the 9/11 attacks in Malaysia (see January 5-8, 2000) and is accused of involvement in many other plots, including the 2002 Bali bombings (see October 12, 2002). Khallad bin Attash (a.k.a. Tawfiq bin Attash) (Yemeni). He also attended a key planning meeting for the 9/11 attacks in Malaysia (see January 5-8, 2000) and had a role in other plots such as the 2000 USS Cole bombing (see October 12, 2000). Ali Abdul Aziz Ali (Pakistani, raised in Kuwait). He allegedly helped finance the 9/11 attacks and arranged transportation for some hijackers. His uncle is KSM. Ramzi bin al-Shibh (Yemeni). A member of the Hamburg al-Qaeda cell with Mohamed Atta and other 9/11 hijackers. The CIA calls him the “primary communications intermediary” between the hijackers and KSM. He also attended a key planning meeting for the 9/11 attacks in Malaysia (see January 5-8, 2000). Abd al-Rahim al-Nashiri (Saudi). He is said to have been one of the masterminds of the USS Cole bombing (see October 12, 2000). He also attended a key planning meeting for the 9/11 attacks in Malaysia (see January 5-8, 2000).
The remaining seven suspects are alleged to have been involved in other al-Qaeda plots: Abu Zubaida (Palestinian, raised in Saudi Arabia). He is said to be a facilitator who helped make travel arrangements for al-Qaeda operatives. He is also alleged to have organized a series of planned millennium attacks. Ahmed Khalfan Ghailani (Tanzanian). He was indicted for a role in the 1998 African embassy bombings (see 10:35-10:39 a.m., August 7, 1998). He is also said to be an expert document forger. Majid Khan (Pakistani). He lived in the US since 1996 and is said to have worked with KSM on some US bomb plots (see March 5, 2003). Abu Faraj al-Libbi (a.k.a. Mustafa al-‘Uzayti) (Libyan). He allegedly became al-Qaeda’s top operations officer after KSM was captured. Mohamad Farik Amin (a.k.a. Zubair) (Malaysian). He is a key Hambali associate and was allegedly tapped for a suicide mission targeting Los Angeles. Mohammed Nazir Bin Lep (a.k.a. Lillie) (Malaysian). He is a key Hambali associate. He is accused of providing funds for the 2003 bombing of the Marriott hotel in Jakarta, Indonesia (see August 5, 2003). He was allegedly tapped for a suicide mission targeting Los Angeles. Gouled Hassan Dourad (Somali). He allegedly scouted a US military base in Djibouti for a planned terrorist attack.
The fourteen are expected to go on trial in 2007. [Knight Ridder, 9/6/2006; Central Intelligence Agency, 9/6/2006; USA Today, 9/7/2006]
September 6, 2006: Bush Admits Existence of Secret CIA Prisons, Announces Plans to Try Top Al-Qaeda Leaders in Military Tribunals
In a speech, President Bush acknowledges a network of secret CIA prisons and announces plans to try 14 top al-Qaeda terrorist suspects in military tribunals. [Knight Ridder, 9/6/2006]
Admits Existence of Detainees in CIA Custody – Bush tells his listeners: “In addition to the terrorists held at Guantanamo, a small number of suspected terrorist leaders and operatives captured during the war have been held and questioned outside the United States, in a separate program operated by the Central Intelligence Agency.… Many specifics of this program, including where these detainees have been held and the details of their confinement, cannot be divulged.… We knew that Abu Zubaida (see March 28, 2002) had more information that could save innocent lives, but he stopped talking.… As his questioning proceeded, it became clear that he had received training on how to resist interrogation. And so the CIA used an alternative set of procedures… The procedures were tough, and they were safe, and lawful, and necessary.… These procedures were designed to be safe, to comply with our laws, our Constitution, and our treaty obligations. The Department of Justice reviewed the authorized methods extensively and determined them to be lawful. I cannot describe the specific methods used—I think you understand why.” Bush then adds that Zubaida “began to provide information on key al-Qaeda operatives, including information that helped us find and capture more of those responsible for the attacks on September 11” (see June 2002). Another high-value detainee, 9/11 planner Khalid Shaikh Mohammed (see Shortly After February 29 or March 1, 2003), provided “many details of other plots to kill innocent Americans” (see March 7 – Mid-April, 2003 and August 6, 2007). [Vanity Fair, 12/16/2008; New York Review of Books, 3/15/2009] The 14 prisoners will be put on trial as soon as Congress enacts the Military Commissions Act (MCA—see October 17, 2006), which he is sending to Congress for its approval today. [Savage, 2007, pp. 308-309]
Political Reasons to Acknowledge CIA Prisons – The US government has never officially acknowledged the existence of the CIA prisons before, despite numerous media accounts about them. Bush’s speech comes less than two months before midterm Congressional elections and also comes as the White House is preparing new legislation to legalize the CIA’s detention program and shield US officials from prosecution for possible war crimes. Knight Ridder comments that the speech “appeared to be intended to give him more leverage in his negotiations with Congress over how to try suspected terrorists.… In addition to the potential political benefits, Bush had other reasons to make the program public. A Supreme Court ruling in June struck down the administration’s plan to bring terrorist suspects before military tribunals and called into question the legality of secret CIA detentions.” [Knight Ridder, 9/6/2006]
Sites Closed Down? – Other administration officials say the CIA prison network has been closed down, at least for the time being. (In fact, it will be reopened a short time later (see Autumn 2006-Late April 2007).) Reportedly, “fewer than 100” suspects had ever been in CIA custody. It is not known who they were or what happened to all of them, but most of them reportedly were returned to their home countries for prosecution. Fourteen “high-value” suspects, including accused 9/11 mastermind Khalid Shaikh Mohammed, were transferred from the secret CIA prisons to the prison in Guantanamo, Cuba in the days just prior to Bush’s speech (see September 2-3, 2006).
Torture is ‘against [US] Values’ – Bush says: “I want to be absolutely clear with our people and the world: The United States does not torture. It’s against our laws, and it’s against our values. I have not authorized it—and I will not authorize it.” However, he says the Geneva Conventions’ prohibition against “humiliating and degrading treatment” could potentially cause legal problems for CIA interrogators. Other administration officials say harsh interrogation techniques such as waterboarding were used in the CIA prisons. Such techniques are considered by many to be forms of torture. Bush claims that information gleaned from interrogations in the secret prisons helped thwart attacks on the US and provided valuable information about al-Qaeda operations around the world. [Knight Ridder, 9/6/2006; Washington Post, 9/7/2006]
Shortly After September 6, 2006: Red Cross Interviews of Top Al-Qaeda Prisoners Indicate They Were Illegally Tortured by CIA
Shortly after 14 high-ranking al-Qaeda prisoners are transferred from secret CIA prisons to the US-controlled Guantanamo prison in Cuba (see September 2-3, 2006), the International Committee of the Red Cross is finally allowed to interview them. The prisoners include 9/11 mastermind Khalid Shaikh Mohammed, Ramzi bin al-Shibh, Hambali, and Abu Zubaida. The Red Cross has a policy of not publicizing or commenting its findings. However, some US officials are shown the report on the interviews with these prisoners and apparently some of these officials leak information to the New Yorker about one year later. The New Yorker will report, “Congressional and other Washington sources familiar with the report said that it harshly criticized the CIA’s practices. One of the sources said that the Red Cross described the agency’s detention and interrogation methods as tantamount to torture, and declared that American officials responsible for the abusive treatment could have committed serious crimes. The source said the report warned that these officials may have committed ‘grave breaches’ of the Geneva Conventions, and may have violated the US Torture Act, which Congress passed in 1994. The conclusions of the Red Cross, which is known for its credibility and caution, could have potentially devastating legal ramifications.” [New Yorker, 8/6/2007]
September 8, 2006: Senate Investigation Finds No Evidence Iraqi Government Used Salman Pak to Train Terrorists
The Senate Intelligence Committee, reporting on the pre-invasion intelligence on Iraq, finds that the US intelligence community had no evidence whatsoever of terrorist training facilities or activities at Iraq’s Salman Pak military base. The report says, “Postwar findings support the April 2002 Defense Intelligence Agency (DIA) assessment that there was no credible reporting on al-Qaeda training at Salman Pak or anywhere else in Iraq. There have been no credible reports since the war that Iraq trained al-Qaeda operatives at Salman Pak to conduct or support transnational terrorist operations.” The report will note testimony from both CIA and DIA officials that found “no indications that training of al-Qaeda linked individuals took place there.” The DIA told the committee in June 2006 that it has “no credible reports that non-Iraqis were trained to conduct or support transnational terrorist operations at Salman Pak after 1991.” [Senate Intelligence Committee, 9/8/2006 
] The base was found to be just what the Iraqis said it was: a training camp for counterterrorism operations, focused on foiling terrorist hijackings of jetliners (see April 6, 2003).
Autumn 2006-Late April 2007: Al-Qaeda Leader Is Kept in Secret CIA Prison, Revealing that CIA Prison System Is Still Operating
In autumn 2006, Abd al-Hadi al-Iraqi, said to be an adviser to Osama bin Laden, is captured and then detained in a secret CIA prison (see Autumn 2006). President Bush announced on September 6, 2006 that the secret CIA prisons were emptied, at least temporarily (see September 2-3, 2006 and September 6, 2006), and it is not known if al-Hadi is transferred to CIA custody before or after this announcement. The CIA keeps al-Hadi’s detention secret from not only the public but also from the Red Cross until late April 2007, when it is publicly announced that al-Hadi has been transferred to the US military prison at Guantanamo. Only then is the Red Cross allowed to examine him. President Bush’s September 2006 announcement was in response to a US Supreme Court decision that rules that all detainees, including those like al-Hadi held in secret CIA prisons, are protected by some provisions of the Geneva Conventions. Then in October 2006 Congress passed the Military Commissions Act, which forbids abuse of all detainees in US custody, including those in CIA custody. The CIA claims that it has no legal responsibility to alert the Red Cross about detainees such as al-Hadi, but without notifying watchdog organizations such as the Red Cross, there is no way to really know if detainees being held by the CIA are being illegally abused or not. Mary Ellen O’Connell, a professor of international law at Notre Dame Law School, says al-Hadi’s case raises the possibility that President Bush has secretly given the CIA a new mandate to operate outside the constraints of the Military Commissions Act: “This suggests that the president has signed some sort of additional authority for the CIA.” [Salon, 5/22/2007]
October 26, 2006: Bush Administration Seeks to Prevent Detainee from Revealing ‘Alternative Interrogation Methods’
The Bush administration submits documents to US District Judge Reggie B. Walton arguing that Majid Khan, a Guatanamo detainee who was held in the secret CIA prison system for three years, cannot be allowed access to lawyers because he may reveal what interrogation techniques were used on him. CIA Information Review Officer Marilyn A. Dorn says in an affidavit that since “detained by CIA in this program, he may have come into possession of information, including locations of detention, conditions of detention, and alternative interrogation techniques that is classified at the TOP SECRET//SCI [sensitive compartmented information] level.” [Washington Post, 11/4/2006]
