A Pakistani-based proliferation network centered around nuclear scientist A. Q. Khan and the ISI intelligence agency begins to use Turkish fronts to acquire technology in the US. This move is made because it is thought Turks are less likely to attract suspicion than Pakistanis. At one point the operation is headed by ISI Director Lt. Gen. Mahmood Ahmed. According to FBI whistleblower Sibel Edmonds, intercepted communications show Mahmood and his colleagues stationed in Washington are in constant contact with attachés at the Turkish embassy. Edmonds will also say that venues such as the American Turkish Council (ATC), a Washington-based lobby group, are used for handovers, and packages containing nuclear secrets are then delivered by Turkish operatives, using their cover as members of the diplomatic and military community, to contacts at the Pakistani embassy in Washington. Edmonds will also allege: “Certain greedy Turkish operators would make copies of the material and look around for buyers. They had agents who would find potential buyers.” [Sunday Times (London), 1/6/2008]
October 12, 1999: General Musharraf Takes Control of Pakistan
Gen. Pervez Musharraf becomes leader of Pakistan in a coup, ousting Prime Minister Nawaz Sharif. One major reason for the coup is the ISI (Pakistan’s intelligence agency) felt Sharif had to go “out of fear that he might buckle to American pressure and reverse Pakistan’s policy [of supporting] the Taliban.” [New York Times, 12/8/2001] Shortly thereafter, Musharraf replaces the leader of the ISI, Brig Imtiaz, because of his close ties to the previous leader. Imtiaz is arrested and convicted of “having assets disproportionate to his known sources of income.” It is later revealed that he was keeping tens of millions of dollars earned from heroin smuggling in a Deutsche Bank account. [Financial Times, 8/10/2001] Lieutenant General Mahmood Ahmed, a close ally of Musharraf, is instrumental in the success of the coup. Ahmed actually secured the capital and detained Sharif, but then honored the chain of command and stepped aside so Musharraf, as head of the military, could take over. Ahmed is rewarded by being made the new director of the ISI. [Guardian, 10/9/2001; Coll, 2004, pp. 504-505]
Spring 2000: ISI Director Said to Become Fundamentalist Muslim
Lt. Gen. Mahmood Ahmed, director of the Pakistani ISI since October 1999 (see October 12, 1999), is not considered especially religious. However, around this time he begins telling his colleagues that he has become a “born-again Muslim.” While he doesn’t make open gestures such as growing a beard, when US intelligence learns about this talk they find it foreboding and wonder what its impact on the ISI’s relations with the Taliban will be. Perhaps not coincidentally, around this time he begins meeting less frequently with CIA liaisons and becomes less cooperative with the US. [Coll, 2004, pp. 510-511] But if Mahmood becomes a fundamentalist Muslim, that would not be very unique in the ISI. As Slate will write shortly after 9/11, “many in the ISI loathe the United States. They view America as an unreliable and duplicitous ally, being especially resentful of the 1990 sanctions, which came one year after the Soviets pulled out of Afghanistan. Furthermore, the ISI is dominated by Pashtuns, the same tribe that is the Taliban’s base of support across the border in Afghanistan. Partly because of its family, clan, and business ties to the Taliban, the ISI, even more than Pakistani society in general, has become increasingly enamored of radical Islam in recent years.” [Slate, 10/9/2001]
April 4, 2000: ISI Director Visits Washington and Is Told to Give Warning to Taliban
ISI Director and “leading Taliban supporter” Lt. Gen. Mahmood Ahmed visits Washington. He meets officials at the CIA and the White House. In a message meant for both Pakistan and the Taliban, US officials tell him that al-Qaeda has killed Americans and “people who support those people will be treated as our enemies.” [Washington Post, 12/19/2001; Coll, 2004, pp. 508-510] US Undersecretary of State Thomas Pickering bluntly tells Mahmood, “You are in bed with those who threaten us.” [Rashid, 2008, pp. 409] The US threatens to support the Northern Alliance, who are still engaged in a civil war with the Taliban. A short time later, Mahmood goes to Afghanistan and delivers this message to Taliban leader Mullah Omar. However, no actual US action, military or otherwise, is taken against either the Taliban or Pakistan. Author Steve Coll will later note that these US threats were just bluffs since the Clinton administration was not seriously considering a change of policy. [Washington Post, 12/19/2001; Coll, 2004, pp. 508-510]
Summer 2000: Saeed Sheikh Frequently Calls ISI Director
In 2002, French author Bernard-Henri Levy is presented evidence by government officials in New Delhi, India, that Saeed Sheikh makes repeated calls to ISI Director Lt. Gen. Mahmood Ahmed during the summer of 2000. Later, Levy gets unofficial confirmation from sources in Washington regarding these calls that the information he was given in India is correct. He notes that someone in the United Arab Emirates using a variety of aliases sends Mohamed Atta slightly over $100,000 between June and September of this year (see June 29, 2000-September 18, 2000 and (July-August 2000)), and the timing of these phone calls and the money transfers may have been the source of news reports that Mahmood Ahmed ordered Saeed Sheikh to send $100,000 to Mohamed Atta (see October 7, 2001). However, he also notes that there is evidence of Sheikh sending Atta $100,000 in August 2001 (see Early August 2001), so the reports could refer to that, or both $100,000 transfers could involve Mahmood Ahmed, Saeed Sheikh, and Mohamed Atta. [Levy, 2003, pp. 320-324]
June 29, 2000-September 18, 2000: Hijackers Receive $100,000 in Funding from United Arab Emirates Location
Hijackers Mohamed Atta and Marwan Alshehhi receive a series of five money transfers from the United Arab Emirates: 
On June 29, $5,000 is wired by a person using the alias “Isam Mansur” to a Western Union facility in New York, where Alshehhi picks it up; On July 18, $10,000 is wired to Atta and Alshehhi’s joint account at SunTrust from the UAE Exchange Centre in Bur Dubai by a person using the alias “Isam Mansur”; On August 5, $9,500 is wired to the joint account from the UAE Exchange Centre by a person using the alias “Isam Mansour”; On August 29, $20,000 is wired to the joint account from the UAE Exchange Centre by a person using the alias “Mr. Ali”; On September 17 $70,000 is wired to the joint account from the UAE Exchange Centre by a person using the alias “Hani (Fawar Trading).” Some sources suggest a suspicious activity report was generated about this transaction (see (Late September 2000)). [Financial Times, 11/29/2001; Newsweek, 12/2/2001; New York Times, 12/10/2001; MSNBC, 12/11/2001; US Congress, 9/26/2002; 9/11 Commission, 8/21/2004, pp. 134-5 
; US District Court for the Eastern District of Virginia; Alexandria Division, 7/31/2006 ] Hijackers Nawaf Alhazmi and Khalid Almihdhar previously received a transfer from the United Arab Emirates from a “Mr. Ali” (see April 16-18, 2000). The 9/11 Commission say this money was sent by Ali Abdul Aziz Ali (a.k.a. Ammar al-Baluchi), a nephew of 9/11 mastermind Khalid Shaikh Mohammed. [9/11 Commission, 8/21/2004, pp. 133-5 ] Although he denies making the $5,000 transfer to Nawaf Alhazmi, Ali will admit sending Alshehhi these amounts and say that the money was Alshehhi’s (see March 30, 2007). He also admits receiving 16 phone calls from Alshehhi around this time (see June 4, 2000-September 11, 2001). [US Department of Defense, 4/12/2007 ] The hijackers may also receive another $100,000 around this time (see (July-August 2000)). It is suggested that Saeed Sheikh, who wires the hijackers money in the summer of 2001 (see Early August 2001), may be involved in one or both of these transfers. For example, French author Bernard-Henri Levy later claims to have evidence from sources inside both Indian and US governments of phone calls between Sheikh and Mahmood Ahmed, head of Pakistan’s Inter-Services Intelligence agency, during this same time period, and he sees a connection between the timing of the calls and the money transfers (see Summer 2000). [Frontline, 10/13/2001; Daily Excelsior (Jammu), 10/18/2001; Levy, 2003, pp. 320-324]
March 1, 2001: Taliban Disregard International Opinion and Destroy Giant Buddha Statues
The Taliban begins blowing up two giant stone Buddhas of Bamiyan—ancient statues carved into an Afghan mountainside, which are considered priceless treasures. They face great international condemnation in response, but no longer seem to be courting international recognition. Apparently, even ISI efforts to dissuade them fail. [Time, 8/12/2002; Time, 8/12/2002] Pakistan President Pervez Musharraf wrote Taliban head Mullah Omar a four-page letter urging him not to blow up the statues, and the letter was secretly hand-delivered to Omar by IS Director Lt. Gen. Mahmood Ahmed, but the letter had no effect. [Rashid, 2008, pp. 409] Omar had previously announced the statues would not be harmed and even opened a National Museum in 2000. The change in policy appears to be due to bin Laden’s growing influence. Journalist Kathy Gannon will later write, “bin Laden’s hardliner rhetoric set the policy, and he campaigned vigorously for the destruction of the statues.” The destruction of the statues further isolates the Taliban internationally, leaving them more dependent on bin Laden’s generosity. [Gannon, 2005, pp. 79-81]
May 2001: CIA Director Tenet Secretly Visits Pakistan, but ISI Director Refuses to Share Information about Bin Laden
Deputy Secretary of State Richard Armitage, a former covert operative and Navy Seal, travels to India on a publicized tour while CIA Director Tenet makes a quiet visit to Pakistan to meet with President Pervez Musharraf. Armitage has long and deep Pakistani intelligence connections (as well as a role in the Iran-Contra affair). While in Pakistan, Tenet, in what was described as “an unusually long meeting,” also secretly meets with his Pakistani counterpart, ISI Director Lt. Gen. Mahmood Ahmed. [SAPRA (New Delhi), 5/22/2001] According to a senior ISI officer in 2006, Tenet urges Mahmood to trade information on Osama bin Laden. However, Mahmood does not cooperate. [Levy and Scott-Clark, 2007, pp. 309, 520]
Summer 2001: Pakistani Intelligence Protects Al-Qaeda Leader from Arrest
The Pakistani ISI allows an al-Qaeda leader to escape arrest. Egyptian investigators are looking for Ahmed Said Khadr, because he is wanted for funding the bombing of the Egyptian embassy in Islamabad, Pakistan, in 1995 (see November 19, 1995). [Time, 5/6/2002; National Post, 10/14/2003] Khadr, a Canadian citizen, had been arrested in Pakistan shortly after the bombing but was then let go after a hunger strike and an appeal by the Canadian government. He runs the Pakistan office of a Canadian charity called Human Concern International. [Canadian Broadcasting Corporation, 4/20/2006] A 1996 CIA report that referred to Khadr called this a charity front that funds radical militants (see January 1996). Khadr’s name appeared on a list of top al-Qaeda suspects issued by the United Nations in 1999. [Canadian Broadcasting Corporation, 3/3/2004] Egyptians surround the safe house in Pakistan where Khadr is hiding. They notify the ISI to help arrest him, and ISI Director Mahmood Ahmed promises swift action. Instead, a car sent by the ISI filled with Taliban and having diplomatic plates arrives, grabs Khadr, and drives him to safety in Afghanistan. Time magazine will later comment: “It was no surprise to foreign spooks that the ISI let [him] escape from Peshawar. He knew too much, they say, about the ISI’s alleged ties with al-Qaeda.” [Time, 5/6/2002] Khadr will be killed in an October 2003 shootout with the Pakistani Army (see October 2, 2003). After his death, a sympathetic jihadist group will refer to him as a “founding member” of al-Qaeda. [National Post, 10/14/2003; Canadian Broadcasting Corporation, 4/20/2006]
Between Mid-August and September 10, 2001: ISI Director Learns Pakistani Nuclear Scientists Are Helping Al-Qaeda, but Fails to Take Action or Warn US
Some time before 9/11, ISI Director Lt. Gen. Mahmood Ahmed learns that two prominent Pakistani nuclear scientists met with Osama bin Laden and Ayman al-Zawahiri in Afghanistan in mid-August 2001. Bin Laden revealed to the two scientists, Sultan Bashiruddin Mahmood and Chaudiri Abdul Majeed, that he had acquired nuclear material and wanted their help to turn it into a weapon (see Mid-August 2001). ISI Director Mahmood is said to have learned about this through military contacts, as several Pakistani generals sit on the board of directors of a charity run by the two scientists that assists the Taliban. For instance, Hamid Gul, a former director of the ISI, is the charity’s honorary patron and was in Afghanistan at the time of the meeting. However, the ISI does not warn the US or take any action against the scientists or their charity. [Levy and Scott-Clark, 2007, pp. 310-311]
