At some point in 2006, an unnamed senior ISI (Pakistani intelligence) official admits that militant leader Jalaluddin Haqqani is a Pakistani asset. The official makes the comment after being asked by a New York Times reporter why the Pakistani military has not moved against Haqqani. Haqqani is head of the Haqqani network, a semi-autonomous branch of the Taliban, based in Pakistan, that is launching attacks against US forces in Afghanistan. [New York Times, 6/17/2008] In 2008, US intelligence will similarly overhear the head of Pakistan’s military call Haqqani a “strategic asset” (see May 2008).
January 13, 2006: US Missile Strike Fails to Kill Al-Zawahiri or Any Other Al-Qaeda Leaders in Pakistan
The US fires a missile from a Predator drone at a Pakistani village named Damadola, in the tribal region near the Afghanistan border. Apparently, al-Qaeda’s number two leader, Ayman al-Zawahri, is targeted but not killed. Thirteen civilians, including women and children, are killed. Pakistani officials say four al-Qaeda operatives may have been killed as well, including bomb maker Midhat Mursi (a.k.a. Abu Khabab al-Masri), who has a $5 million bountry on his head. After the attack, villagers insist no members of al-Qaeda were anywhere near the village when it was hit. [ABC News, 1/18/2006; Associated Press, 1/22/2006] US and Pakistani officials later say that no al-Qaeda leaders were killed in the strike, only local villagers. It appears that the intelligence tip that led to the strike was bad, and al-Zawahiri and the others were never there in the first place. [Washington Post, 9/9/2007] The attack leads to a surge in support for al-Qaeda in Pakistan, including many marches of support near the targeted area. [ABC News, 1/18/2006; Associated Press, 1/22/2006] Pakistani President Pervez Musharraf condemns the attack as a violation of sovereignty and says it “was definitely not coordinated with [Pakistan].” [Washington Post, 1/31/2006] Al-Zawahiri appears in a video later in the month, taunting the US for failing to kill him in the raid. [BBC, 1/30/2006]
January 26, 2006: Pakistan’s Support for Resurgent Taliban Persists, Newspaper Says
A New York Times investigation along the Afghan-Pakistan border finds not-so-hidden evidence of continued Pakistani support for the growing Taliban insurgency in Afghanistan. Pakistan’s intelligence agencies are said to be using a network of religious political parties to attract and then pressure young men into joining the jihad in Afghanistan or in Kashmir. The agencies are believed to be preparing for the day when NATO troops leave the country and hope to re-install a pro-Pakistan government in Kabul. [New York Times, 1/21/2006]
February 2006: US Military Gives Bin Laden Search Surprisingly Low Priority
Counterterrorism expert Micah Zenko will later claim that in February 2006, an unnamed senior civilian official serving at US Central Command tells him that he has been disappointed to learn the search for Osama bin Laden is being worked at a lower level than he would have suspected. Central Command, which covers the US military’s operations in the Middle East and South Asia, has other issues that are deemed more important. [New York Times, 5/3/2011]
May 2, 2006: Taliban Leaders Said to Be Living Openly in Pakistani Border City with Pakistani Government Assistance
The Christian Science Monitor reports: “Taliban leaders strut openly around Quetta, Pakistan, where they are provided with offices and government-issued weapons authorization cards; Pakistani army officers are detailed to Taliban training camps; and Pakistani border guards constantly wave self-proclaimed Taliban through checkpoints into Afghanistan.” A Monitor reporter who lives in Kandahar, Afghanistan, notes that the result is that people there “have reached an astonishing conclusion: The United States must be in league with the Taliban… In other words, in a stunning irony, much of this city, the Taliban’s former stronghold, is disgusted with the Americans not because of their Western culture, but because of their apparent complicity with Islamist extremists.” [Christian Science Monitor, 5/2/2006] CNN will similarly report in September 2006 that Taliban head Mullah Omar and most other top Taliban leaders are living in Quetta (see September 12, 2006).
May 29, 2006: Kabul Riots Suggest Discontent over Development and Governance
A US Army truck in a convoy careens out of control in Kabul, Afghanistan, killing at least three locals. Witnesses see the incident as symbolic of lack respect for the Afghan populace and rumors quickly swirl that it was intentional. Angry crowds form and begin pelting the rest of the convoy with rocks. US and/or Afghan soldiers open fire on the crowd and kill about six Afghans. This further enrages the populace, leading to rioting and looting all over Kabul for hours. Looters destroy businesses, Western non-profit offices, and even lay siege to the Interior Ministry for a time. NATO peacekeeping troops stay in their compounds and Afghan security forces are ineffectual. Officially, 17 are killed in the riots, but informed observers believe the death count is close to 100. Afghan member of parliament Dr. Ramazan Bashar Dost says that the people are angry at perceived price gouging by Western contractors and non-profits, and what is seen as poor results for all the billions of dollars spent. He says, “The problem is that the [non-profits] work within the system of corruption that plagues Afghanistan. They pay the bribes to the officials and even to Western contractors. So people see them as part of the same system as the corrupt government.” [Salon, 6/14/2006; New York Times, 8/23/2006] Afghan President Hamid Karzai responds by appointing a new police chief and other top police officers known for their ties to organized crime. [New York Times, 8/23/2006]
Mid-2006: US Transfers ‘Ghost’ Prisoner Ghul to Pakistani Custody
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).
July 9, 2006: Joint US, NATO, and Afghan Report Reveals ISI Is Paying and Training Taliban to Fight in Afghanistan, but US Takes No Action
In June 2006, the US, NATO, and Afghanistan’s intelligence agency compile a secret report on the Taliban. The report is discussed on July 9 at a private meeting of officials from Western countries and Afghanistan, chaired by Afghan President Hamid Karzai. The report goes further than any previous report in describing the Pakistani government’s involvement in supporting the Taliban. It states, “ISI operatives reportedly pay a significant number of Taliban living/ operating in both Pakistan and Afghanistan to fight.… A large number of those fighting are doing so under duress as a result of pressure from the ISI. The insurgency cannot survive without its sanctuary in Pakistan, which provides freedom of movement, communications for command and control, and a secure environment for collaboration with foreign extremist groups. The sanctuary of Pakistan provides a seemingly endless supply of potential new recruits for the insurgency.” The report also states that at least four of the Taliban’s top leaders are living in Pakistan. But despite the US involvement in creating the report, US diplomacy generally remains in denial about Pakistan’s double dealing. President Bush not only fails to successfully pressure Pakistan on the issue, but even continues to praise Pakistani President Pervez Musharraf. The report is not leaked to the press at the time. [Rashid, 2008, pp. 367-368] In September 2006, when Pakistan announces a deal with militants in the tribal region of Waziristan, the heart of al-Qaeda’s safe haven, Bush publicly supports the deal (see September 5, 2006 and September 7, 2006).
September 5, 2006: Deal with Pakistani Government Gives Al-Qaeda and Taliban Safe Haven in Tribal Region of North Waziristan
The government of Pakistan signs an agreement known as the Waziristan Accord with rebels in the tribal area of Pakistan near the border of Afghanistan known as Waziristan. This is the area where the Taliban and al-Qaeda have a strong influence and many believe al-Qaeda’s top leaders Osama bin Laden and Ayman al-Zawahiri are hiding there. The accord effectively puts an end to fighting between the Pakistani army and the rebels. Details of the accord are published in a Pakistani newspaper the next day. The main points include: 
The Pakistani government agrees to stop attacks in Waziristan. Militants are to cease cross-border movement into and out of Afghanistan. Foreign jihadists will have to leave Pakistan, but “those who cannot leave will be allowed to live peacefully, respecting the law of the land and the agreement.” Area check-points and border patrols will be manned by a tribal force and the Pakistan army will withdraw from control points. No parallel administration will be established in the area, but Pakistan law will remain in force. Tribal leaders will ensure that no one attacks government personnel or damages state property. The Pakistani government will release captured militants and will pay compensation for property damage and the deaths of innocent civilians. [Dawn (Karachi), 9/6/2006] The deal is negotiated and signed by Gen. Ali Jan Orakzai, who had become the governor of the nearby North-West Frontier Province some months earlier. Orakzai, a close friend of Pakistani President Pervez Musharraf, is known to hate the US and NATO and admire militant groups such as the Taliban (see Late 2002-Late 2003). [New York Times, 6/30/2008] Two days later, President Bush publicly supports the deal (see September 7, 2006). The Wall Street Journal comments that Musharraf decided to approve the deal in order to take care of “an even bigger security problem: a growing rebellion in the resource-rich province of Baluchistan.” He does not have the forces to deal with widespread violence in both regions. [Wall Street Journal, 9/8/2006]
A similar deal was made with South Waziristan in February 2005 (see February 7, 2005). The agreement will soon be seen as a big success for al-Qaeda and the Taliban. In July 2007, the Washington Post will report that senior US intelligence officials attribute “the resurgence of bin Laden’s organization almost entirely to its protected safe haven among tribal groups in North Waziristan…” (see July 18, 2007). The same month, the Bush administration will publicly call the accord a failure as it collapses amidst an all out fight between the government and militants in Pakistan (see July 11-Late July, 2007). [Washington Post, 7/18/2007]
September 7, 2006: President Bush Supports Pakistan’s Deal with Taliban-linked Militants
On September 5, 2006, the government of Pakistan signs an agreement known as the Waziristan Accord with militants in the tribal area of Pakistan near the border of Afghanistan known as Waziristan (see September 5, 2006). Two days later, Pakistani President Pervez Musharraf and Lt. Gen. Ali Jan Orakzai come to the White House to meet with President Bush about the deal. Orakzai is the military commander of the region encompassing the region. He reportedly hates the US and sympathizes with the Taliban, calling them a “national liberation movement” (see Late 2002-Late 2003). In a presentation to Bush, Orakzai advocates a strategy that would rely even more heavily on cease-fires, and says striking deals with the Taliban inside Afghanistan could allow US forces to withdraw from Afghanistan within seven years. Bush supports the deal, saying in public that same day that it would not create safe havens for the Taliban and could even offer “alternatives to violence and terror.” He does add the cautionary note, “You know we are watching this very carefully, obviously.” [Rashid, 2008, pp. 277; New York Times, 6/30/2008] But three months later, the US State Department will publicly deem the deal a failure for US policy (see November-December 2006). Some US officials will begin to refer to Orakzai as a “snake oil salesman.” [New York Times, 6/30/2008]
