Since being defeated in Tora Bora, Afghanistan, in late 2001, al-Qaeda has made a safe haven in the Pakistani tribal region of South Waziristan (see December 10, 2001 and Late May 2002). But in April 2004, the Pakistani army begins attacking militants there (see March 18- April 24, 2004 and April 24-June 18, 2004). The army is defeated, but rapidly increases its troops in South Waziristan from less than 10,000 militia soldiers based only in the main town before the fighting began to 80,000 throughout the region. As a result, most of the al-Qaeda militants simply move from South Waziristan to North Waziristan. There is no similar increase in troop strength in North Waziristan, so al-Qaeda is able to reestablish a safe haven there. [Rashid, 2008, pp. 274] In February 2005, the army will strike a deal with the remaining militants in South Waziristan and withdraw all its troops from there, allowing al-Qaeda to reestablish themselves there as well (see February 7, 2005).
July 12, 2004: 9/11 Commission Staff Meet with Navy Officer Involved with Able Danger Unit
Ten days before the 9/11 Commission releases its final report, a senior member of its staff, Dietrich Snell, accompanied by another commission staff member, meets at one of the commission’s Washington, DC offices with a US Navy officer who worked with a US Army intelligence program called Able Danger, which had been tasked with assembling information about al-Qaeda networks around the world. This officer, Captain Scott Phillpott, tells them he saw an Able Danger document in 2000 that described Mohamed Atta as part of a Brooklyn al-Qaeda cell. He complains that this information about Atta, and information about other alleged members of the Brooklyn cell, was deleted from the document soon after he saw it, due to the concerns of Department of Defense lawyers. However, despite having this meeting with Phillpott, and having met previously with an Army intelligence officer who was also involved with Able Danger (see October 21, 2003), the 9/11 Commission makes no mention of the unit in their final report. The commissioners later claim that Phillpott’s information “[does] not mesh with other conclusions” they are drawing from their investigation. Consequently, the commission staff conclude “that the officer’s account [is] not sufficiently reliable to warrant revision of the report or further investigation.” Able Danger is not mentioned in their final report, they claim, because “the operation itself did not turn out to be historically significant.”
[Associated Press, 8/11/2005; New York Times, 8/11/2005; Thomas H. Kean and Lee H. Hamilton, 8/12/2005 
; New York Times, 8/13/2005; Washington Post, 8/13/2005; New York Times, 8/22/2005] Lt. Col. Anthony Shaffer additionally claims, “Captain Phillpott actually told the 9/11 Commission about the fact that Able Danger discovered information regarding the Cole attack.… There was information that Able Danger found that related to al-Qaeda planning an attack. That information unfortunately didn’t get anywhere either. So that is another clue that was given to the 9/11 Commission to say, hey, this [Able Danger] capability did some stuff, and they chose not to even look at that.” [Jerry Doyle Show, 9/20/2005]
July 13, 2004: Al-Qaeda Computer Expert Arrested with Treasure Trove of Evidence
Muhammad Naeem Noor Khan, a young Pakistani, is arrested in Lahore after six weeks of surveillance by Pakistani authorities in conjunction with US intelligence agencies. The US and Pakistanis learned of Noor Khan after arresting another al-Qaeda suspect, Musaad Aruchi, a month before (see June 12, 2004), and they had been tracking him since then. Noor Khan is taken to a high-security prison by Pakistani authorities, who resisted pressure from the CIA to let them completely handle the operation. [Guardian, 8/8/2004] American intelligence agents find what they later call a “treasure trove” of information in Noor Khan’s computers and documents. [CNN, 8/2/2004] Khan is a communications hub of sorts for al-Qaeda. He is in frequent contact with dozens of other al-Qaeda terrorists around the world and passing messages back and forth from more senior al-Qaeda operatives. Former National Security Council official Gideon Rose will later say, “It is obviously a very serious victory. It is obvious that there is a real find here.” [Guardian, 8/8/2004] Khan, who speaks fluent English, is not just a center for expediting clandestine communications between al-Qaeda leaders and their underlings, but also handles and collates documents, reports, maps, and other information, and sometimes performs his own intelligence-gathering, usually on trips to Britain. [MSNBC, 8/8/2004] Khan’s computer contains detailed surveillance information about five US buildings—the Stock Exchange and Citigroup’s headquarters in New York City, the Prudential building in Newark, and the International Monetary Fund and World Bank headquarters in Washington—all possible targets for future al-Qaeda attacks, though the information is all from 2000 and 2001. Other sites in New York City and San Francisco are mentioned, and meticulous information about London’s Heathrow Airport is also found. Pakistani intelligence officials believe that the information indicates a “present” threat, and so inform their US counterparts. Later in the month, the Pakistanis convince Khan to “turn,” or become a double agent. Khan will subsequently send e-mails to dozens of operatives all requesting that they contact him immediately (see July 24-25, 2004). [Guardian, 8/8/2004]
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]
July 22, 2004: Evidence the ISI Was ‘Fully Involved’ in the 9/11 Plot Is Ignored by 9/11 Commission
UPI reports that the 9/11 Commission has been given a document from a high-level, publicly anonymous source claiming that the Pakistani “ISI was fully involved in devising and helping the entire [9/11 plot].” The document blames Gen. Hamid Gul, a former ISI Director, as being a central participant in the plot. It notes that Gul is a self-avowed “admirer” of bin Laden. An anonymous, ranking CIA official says the CIA considers Gul to be “the most dangerous man” in Pakistan. A senior Pakistani political leader says, “I have reason to believe Hamid Gul was Osama bin Laden’s master planner.” The document further suggests that Pakistan’s appearance of fighting al-Qaeda is merely an elaborate charade, and top military and intelligence officials in Pakistan still closely sympathize with bin Laden’s ideology. [United Press International, 7/22/2004] However, the 9/11 Commission final report released a short time later will fail to mention any of this. [9/11 Commission, 7/24/2004]
July 22, 2004: 9/11 Commission’s Final Report Is Released; Conclusions are ‘Gentle’ on Bush Administration
The 9/11 Commission completes its work and releases its final report. They blame incompetence for the reason why the US government did not prevent the attack. The Washington Post summarizes the report, “The US government was utterly unprepared on Sept. 11, 2001, to protect the American people from al-Qaeda terrorists.” [Washington Post, 7/23/2004] The report itself states, “We believe the 9/11 attacks revealed four kinds of failures: in imagination, policy, capabilities, and management.” [9/11 Commission, 7/24/2004] The Washington Post reports, “Though openly dreaded for months by many Republicans and quietly feared by the White House, the report was much gentler on the Bush administration than they feared. Rather than focus criticism on the Bush administration, the commission spread the blame broadly and evenly across two administrations, the FBI, and Congress.” [Washington Post, 7/23/2004] More to the point, as former counterterrorism “tsar” Richard Clarke notes in a New York Times editorial, “Honorable Commission, Toothless Report,” because the commission wanted a unanimous report from a bipartisan group, “it softened the edges and left it to the public to draw many conclusions.” [New York Times, 7/25/2004] The Washington Post comments, “In many respects, the panel’s work has been closer to the fact-finding, conspiracy-debunking Warren Commission of the mid-1960s, which investigated the assassination of President John F. Kennedy, than to the reform-oriented Church Commission, which exposed assassination plots and CIA abuses during the mid-1970s.” [Washington Post, 7/18/2004]
July 22, 2004: 9/11 Commission Report Fails to Mention Possible ISI Connections to 9/11
Despite previous leaks to the media showing the 9/11 Commission was given information showing Pakistani officials were “up to their eyeballs” in collaboration with the Taliban and al-Qaeda before 9/11 (see June 20, 2004) [Los Angeles Times, 6/14/2004] , and even reports of a document given to the commission claiming the “ISI was fully involved in devising and helping the entire [9/11 plot]” (see July 22, 2004) [United Press International, 7/22/2004] , the 9/11 Commission’s Final Report released on this day rarely mentions the ISI at all. The only significant mention is a brief comment that the ISI was the Taliban’s “primary patron.” ISI Director Lt. Gen. Mahmood Ahmed is mentioned only twice, both in the context of post-9/11 diplomacy. Saeed Sheikh is not mentioned at all. The report notes that details of the 9/11 plot were widely known by the Taliban leadership, but fails to consider if the Taliban shared that knowledge or involvement with their “primary patron.” [9/11 Commission, 7/24/2004] Indeed, far from criticizing Pakistan, the commission praises the country for its support in the war on terrorism, and suggests that the US should greatly increase its foreign aid there. [Associated Press, 7/22/2004]
July 22, 2004: 9/11 Commission Finds No 9/11 Insider Trading
The 9/11 Commission dismisses allegations of insider trading in the days preceding 9/11, in a footnote contained in its final report. According to the report, the put options for the parent companies of United Airlines were placed by a “US-based institutional investor with no conceivable ties to al-Qaeda as part of a trading strategy that also included buying 115,000 shares of American on September 10.” With respect to the highly suspicious trading in the parent company of American Airlines, the Commission states that many of the trades were “traced to a specific US-based options trading newsletter, faxed to its subscribers on Sunday, September 9, which recommended these trades.” According to the Commission: “The SEC and the FBI, aided by other agencies and the securities industry, devoted enormous resources to investigating this issue, including securing the cooperation of many foreign governments. These investigators have found that the apparently suspicious consistently proved innocuous.” [9/11 Commission, 7/24/2004, pp. 499]
July 24-25, 2004: Al-Qaeda Communications Node Is Turned, He Leads to Dozens of Operatives Around World
On July 13, 2004, a young Pakistani al-Qaeda operative named Muhammad Naeem Noor Khan was arrested in Pakistan (see July 13, 2004). US intelligence agents find what they later call a “treasure trove” of information in Noor Khan’s computers and documents. [CNN, 8/2/2004] They realize that Khan has served as a communications hub of sorts for al-Qaeda. He is in frequent contact with dozens of other al-Qaeda terrorists around the world and passing messages back and forth from more senior al-Qaeda operatives. Intelligence agents quickly realize that, through Khan, they can penetrate deep into the core of al-Qaeda’s current operations. Around the weekend of July 24-25, the Pakistanis convince Khan to “turn,” or become a double agent. Khan sends e-mails to dozens of activists in Indonesia, Malaysia, Pakistan, India, Bangladesh, and other countries. He requests that they contact him immediately and reveal where they are. As the emails come back, intelligence agents all over the world go into action to monitor those who have replied to Khan. [Guardian, 8/8/2004] Newsweek later reports that he sends e-mails to at least six contacts in the US, but the results of this are unknown. A senior US intelligence official confirms that Khan contacted people in the US, but believes number is less than six. [MSNBC, 8/8/2004] Some of Khan’s contacts are quickly arrested, including Ahmed Khalfan Ghailani, a Tanzanian wanted since 1998 for his role in the bombing of the US embassy in his home country (see July 25-29, 2004). [Suskind, 2006] Some communications take time to reach him. He is sometimes sent handwritten notes or computer discs from the mountains where bin Laden and other top leaders are hiding out. These are delivered by secretive relays of couriers who never see each other, using dead drops to avoid being traced. Other messages come from far-flung intermediaries who forward e-mail without knowing what it means, where it is going, or who is sending it. [MSNBC, 8/8/2004] However, on August 1, Bush administration officials leak Noor Khan’s name to the press and the New York Times prints his name one day later. This only gives one week for the sting operation to work. Intelligence officials are crushed the operation has to end before it could expose many more al-Qaeda operatives (see August 2, 2004).
July 25-29, 2004: Al-Qaeda Suspect Arrested in Pakistan; Some Allege Announcement Is Timed for Political Effect
Ahmed Khalfan Ghailani, a high-level al-Qaeda operative from Tanzania suspected of participating in the 1998 bombings of US embassies in East Africa, is captured in Gujrat, Pakistan, after a violent standoff with Pakistani police. [CNN, 8/3/2004] Ghailani’s arrest is publicly announced on July 29, four days later. The announcement by Pakistan’s Interior Minister Faisal Hayat is made in an unusual late-night press conference that takes place just hours before John Kerry accepts the Democratic nomination for president. [Salon, 8/17/2004] Pakistani authorities say the announcement of Ghailani’s arrest was delayed four days because of the need to confirm his identity before making the proclamation. [BBC, 7/30/2004] But former Pakistani official Husain Haqqani later claims the announcement was timed to upstage the Kerry speech. [Salon, 8/17/2004; United States Conference on International Religious Freedom, 6/30/2005] An article in the New Republic published earlier in the month reported that the Bush administration was asking Pakistan to make high-profile arrests of al-Qaeda suspects during the Democratic National Convention in order to redirect US media attention from the nomination of John Kerry (see July 8, 2004). [New Republic, 7/29/2004] John Judis, who co-wrote the article predicting such an arrest, says the day after the arrest is announced, “Well, the latest development pretty much confirms what we wrote in the article, which is that there was pressure for Pakistan to produce a high-value target during the last 10 days of July and to announce that arrest.” He also asks why is it “they announced [the arrest] at all? Because when you have somebody who’s been in hiding since 1998, they have an enormous amount of information and contacts. By announcing this guy’s arrest, what you do is you warn off everybody who’s been associated with him from the last five or six years. You tell them that they better get their act together or they are going to be found. So, there’s some, really a lot of questions of why they announced this thing when they did.… It may be in this case that we—that we, and the Pakistanis got somebody and prematurely announced this person’s arrest in order to have an electoral impact.” [Democracy Now!, 7/30/2004]
