Afghanistan, Pakistan, and Turkmenistan reach an agreement in principle to build the Trans-Afghanistan Pipeline, a $3.2 billion project that has been delayed for many years. Skeptics say the project would require an indefinite foreign military presence in Afghanistan. [BBC, 5/30/2002; Associated Press, 12/26/2002; BBC, 12/27/2002] As of mid-2004, construction has yet to begin.
January 18, 2003: Pakistan’s President Warns of Imminent Western Attack
Pakistani President Pervez Musharraf warns of an “impending danger” that Pakistan will become a target of war for “Western forces” after the Iraq crisis. “We will have to work on our own to stave off the danger. Nobody will come to our rescue, not even the Islamic world. We will have to depend on our muscle.”
[Press Trust of India, 1/19/2003; Financial Times, 2/8/2003] Pointing to “a number of recent ‘background briefings’ and ‘leaks’” from the US government, “Pakistani officials fear the Bush administration is planning to change its tune dramatically once the war against Iraq is out of the way.”
[Financial Times, 2/8/2003] Despite evidence that the head of Pakistan’s intelligence agency, the ISI, ordered money given to the hijackers, so far only one partisan newspaper has suggested Pakistan was involved in 9/11. [WorldNetDaily, 1/3/2002]
July 16, 2004: 9/11 Commission Chairman’s Comments Lead to Flurry of Reporting on Iran, None on Pakistan
Shortly before the 9/11 Commission is due to release its final report (see July 22, 2004), Commission Chairman Thomas Kean says, “We believe.… that there were a lot more active contacts, frankly, [between al-Qaeda and] Iran and with Pakistan than there were with Iraq.” [Time, 7/16/2004] This is based on a review of NSA material performed by one commission staffer (see January-June 2004) and a day trip to NSA headquarters by a group of staffers to examine material there (see Between July 1 and July 17, 2004). [Shenon, 2008, pp. 155-7, 370-373] The US media immediately runs prominent stories on the Commission’s evidence regarding Iran and nearly completely ignores evidence regarding Pakistan. The Commission’s final report mentions that around ten of the hijackers passed through Iran in late 2000 and early 2001. At least some Iranian officials turned a blind eye to the passage of al-Qaeda agents, but there was no evidence that the Iranian government had any foreknowledge or involvement in the 9/11 plot (see Mid-July 2004). [Time, 7/16/2004; Reuters, 7/18/2004] In the wake of these findings, President Bush states of Iran, “As to direct connections with September 11, we’re digging into the facts to determine if there was one.” This puts Bush at odds with his own CIA, which has seen no Iran-9/11 ties. [Los Angeles Times, 7/20/2004] Bush has long considered Iran part of his “axis of evil,” and there has been talk of the US attacking or overthrowing the Iranian government. [Reuters, 7/18/2004] Provocative articles appear, such as one in the Daily Telegraph titled, “Now America Accuses Iran of Complicity in World Trade Center Attack.” [Daily Telegraph, 7/18/2004] Yet, while this information on Iran makes front page news in most major newspapers, evidence of a much stronger connection between Pakistan and 9/11 is nearly completely ignored. For instance, only UPI reports on a document suggesting high-level Pakistani involvement in the 9/11 attacks that is revealed this same week. [United Press International, 7/22/2004] Furthermore, the 9/11 Commission’s final report will contain almost nothing on Pakistan’s ties to al-Qaeda, despite evidence given to the Commission that, according to one commissioner speaking to the Los Angeles Times, showed that Pakistan was “up to their eyeballs” in intrigue with al-Qaeda. [Los Angeles Times, 7/16/2004; 9/11 Commission, 7/24/2004]
August 4, 2004: Pakistan Continues to Support the Taliban
The New York Times reports that, “For months Afghan and American officials have complained that even while Pakistan cooperates in the fight against al-Qaeda, militant Islamic groups there are training fighters and sending them into Afghanistan to attack American and Afghan forces.” One prisoner captured by the Afghan government says Pakistan is allowing militant groups to train and organize insurgents to fight in Afghanistan. Groups designated as terrorist organizations by the US and/or Pakistan have simply changed names and continue to operate freely. An anonymous Western diplomat says, “When you talk about Taliban, it’s like fish in a barrel in Pakistan. They train, they rest there. They get support.” The New York Times comments, “Western diplomats in Kabul and Pakistani political analysts have said that Pakistan has continued to allow the Taliban to operate to retain influence in Afghanistan.”
[New York Times, 8/4/2004]
December 14, 2004: Report: US Has Abandoned Its Hunt for Bin Laden
The Daily Telegraph reports that “the search for [bin Laden] the world’s most wanted man has all but come to a halt because of Pakistan’s refusal to permit cross-border raids from Afghanistan, according to CIA officials.” Even spy missions by unmanned Predator drones need Pakistani military approval involving a lengthy chain of command that frequently causes delays. Most accounts have bin Laden still alive and living in the near-lawless Pakistan and Afghanistan border region. US officials believe bin Laden and his deputies are being hidden by sympathetic local tribesmen, who are continuing to fund his operations from opium sales. [Daily Telegraph, 12/14/2004]
Late 2004-Early 2005: Classified US Documents Suggest Pakistan Is Supporting Taliban
Classified US documents later found by reporters (see April 10, 2006) but dating from this time suggest that the Taliban is planning to attack US troops from bases inside Pakistan with the acquiescence or even support of elements within the Pakistani government. For instance, an August 2004 presentation accuses Pakistan of making “false and inaccurate reports of border incidents.” A document from early 2005 mentions that the US military is attempting to stop the flow of weapons to the Taliban from Pakistan and stop infiltration routes from Pakistan. Another document includes a US military commander commenting, “Pakistani border forces [should] cease assisting cross border insurgent activities.” [Los Angeles Times, 4/10/2006] Later in 2005, a report by Congress’ research arm will echo these concerns, stating, “Among the most serious sources of concern is the well-documented past involvement of some members of the Army’s Inter-Services Intelligence (ISI) organization with al-Qaeda and the Taliban, and the possibility that some officers retain sympathies with both groups.” [Los Angeles Times, 4/14/2006]
February 2005: Taliban Leaders and Pakistani Officials Allegedly Meet to Plan More Attacks against US Forces in Afghanistan
A June 2005 Guantanamo file on a relatively low-level Taliban detainee allegedly mentions in passing a February 2005 meeting of militant leaders in Quetta, Pakistan. According to intelligence reports referred to in the file, Mullah Omar, top head of the Taliban, leads the meeting. Other high-level Taliban leaders such as Mullah Akhter Mohammed Osmani also attend. But most interestingly, representatives from the Pakistani government and the ISI, Pakistan’s intelligence agency, are at the meeting as well. In the meeting, “Mullah Omar [tells] the attendees that they should not cooperate with the new infidel government (in Afghanistan) and should keep attacking coalition forces.” The Guantanamo file mentioning the meeting will be leaked to the public in 2011. [Joint Task Force Guantanamo, 6/3/2005 
; Guardian, 4/25/2011]
June 19, 2005: CIA Director Says He Has ‘Excellent Idea’ Where Bin Laden Is Hiding
Asked if he has a good idea where Osama bin Laden is hiding, CIA Director Porter Goss replies: “I have an excellent idea of where he is. What’s the next question?” Although he doesn’t mention the country, Goss implies he is referring to Pakistan. He mentions the “very difficult question of dealing with sanctuaries in sovereign states,” which appears to be a diplomatic way of referring to the tribal region of Pakistan, where many believe bin Laden is located. [BBC, 6/20/2005] Vice President Dick Cheney will make a similar comment several days later (see June 23, 2005).
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).
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]
