Khalid Shaikh Mohammed (KSM) is publicly identified as the “mastermind” behind the 9/11 attacks. He is believed to have arranged the logistics while on the run in Germany, Pakistan, and Afghanistan. In 1996, he had been secretly indicted in the US for his role in Operation Bojinka (see January 6, 1995), and the US began offering a $2 million reward for his capture in 1998 (see January 8, 1998), which increased to $25 million in December 2001. An international warrant for his arrest was issued in November 2000 (see November 17, 2000). [Associated Press, 6/4/2002; New York Times, 6/5/2002] According to the New York Times, “In recent months, American counterintelligence officials have identified a small group of other al-Qaeda lieutenants as the crucial figures behind the Sept. 11 attacks” aside from KSM. They include Mohammed Atef (who is already deceased), Abu Zubaida, and Ayman al-Zawahiri. [New York Times, 6/5/2002] There are conflicting accounts of how much US investigators knew about KSM before 9/11. He is Pakistani, although he was born and raised in Kuwait. [CBS News, 6/5/2002] He is an uncle of Ramzi Yousef, the bomber of the World Trade Center in 1993. [New York Times, 6/5/2002] In April 2002, captured al-Qaeda leader Abu Zubaida confessed that KSM was the 9/11 mastermind (see April 2002). It is not known how much US intelligence knew about KSM’s link to the 9/11 attacks prior that, although at least some was known (see (December 2001)).
June 22, 2002: Al-Qaeda Spokesperson Says Bin Laden and Other Top Leaders Are Still Alive
Al-Qaeda spokesperson Suliman Abu Ghaith allegedly claims that al-Qaeda leaders Osama bin Laden and Ayman al-Zawahiri, plus Taliban leader Mullah Omar, are alive and well. “I want to assure Muslims that Sheik Osama bin Laden… is in good and prosperous health and all what is being rumored about his illness and injury in Tora Bora has no truth,” he says. He adds that al-Qaeda is ready to attack new targets, and says it is responsible for a recent bombing of a synagogue in Djerba, Tunisia (see April 11, 2002). Although he does not explicitly say al-Qaeda was behind the 9/11 attacks, he calls the attacks a “great historic victory that broke the backs of the Americans, the strongest power in this world.” The comments are made in an audiotape played on Al Jazeera. The authenticity of the recording has not been independently confirmed, and Al Jazeera does not explain how it got the recording or when it was made. [Associated Press, 6/22/2002] Abu Ghaith previously issued video recordings of his statements (see October 10, 2001).
September 10, 2002: 10 of Al-Qaeda’s 24 Pre-9/11 Leaders Said to Be Killed or Captured
The New York Times reports that 10 out of the 24 al-Qaeda leaders considered most important by the CIA before 9/11 have been killed or captured. [New York Times, 9/10/2002] The four most important figures considered still at large are: 
Osama bin Laden (Saudi). He will be killed in 2011 (see May 2, 2011). Ayman al-Zawahiri (Egyptian). Khalid Shaikh Mohammed (Kuwaiti/Pakistani). He will be captured in 2003 (see February 29 or March 1, 2003). Saif al-Adel (Egyptian).
Other figures considered still at large are: Abdullah Ahmed Abdullah (Egyptian). Mustafa Muhammad Fadhil (Egyptian). Mushin Musa Matwalli Atwah (Egyptian). He will be killed in 2006 (see April 12, 2006). Usama al-Kini (a.k.a. Fahid Muhammad Ally Msalam) (Kenyan). He will be killed in 2009 (see January 1, 2009). Fazul Abdullah Mohammed (a.k.a. Haroun Fazul) (Comoros Islander). He will be killed in 2011 (see June 10, 2011). Mahfouz Walad Al-Walid (a.k.a. Abu Hafs the Mauritanian) (Mauritanian). Amin ul-Haq (Afghan). Midhat Mursi (Egyptian). He will be killed in 2008 (see July 28, 2008). Anas al-Liby (Libyan). He may have been secretly captured already (see January 20, 2002- March 20, 2002). Suliman abu Ghaith (Kuwaiti). Saad bin Laden (Saudi). He apparently will be killed in 2009 (see July 22, 2009). Mustafa Ahmed al-Hawsawi (Saudi). He will be captured in 2003 (see February 29 or March 1, 2003). [New York Times, 9/10/2002]
The four leaders captured are: Abu Zubaida (Palestinian) (see March 28, 2002). Abdul Rahim al-Sharqawi (Yemeni) (see Late 2001 and February 7, 2002). Ibn al-Shaykh al-Libi (Libyan) (see December 19, 2001). Abu Zubair al-Haili (Saudi) (see June 8, 2002 and After). [New York Times, 9/10/2002]
Five of the six leaders believed killed are: Mohammed Atef (Egyptian) (see November 15, 2001). Abu Jaffa (a.k.a. Abu Jafar al-Jaziri) (Algerian). Abu Salah al-Yemeni (Yemeni). Tariq Anwar al-Sayyid Ahmad (Egyptian). Muhammad Salah (a.k.a. Nasr Fahmi Nasr Hasanayn) (Egyptian). [New York Times, 9/10/2002]
The sixth leader believed killed is not named. One year after 9/11, US intelligence identifies 20 current high-ranking al-Qaeda leaders, though it is not mentioned who the six new leaders are who replaced some of the killed or captured leaders. [New York Times, 9/10/2002] This list of leaders, while instructive, is curiously incomplete because it fails to mention al-Qaeda leaders known as important to US intelligence before 9/11, such as Hambali, Khallad bin Attash, Abd al-Rahim al-Nashiri, Thirwat Salah Shehata, Mustafa Abu al-Yazid, Ahmed Khalfan Ghailani, and Mohammed Jamal Khalifa.
Shortly After February 29 or March 1, 2003: KSM Allegedly Confesses He Has Recently Seen Bin Laden
Shortly after the arrest of 9/11 mastermind Khalid Shaikh Mohammed (KSM) (see February 29 or March 1, 2003), US investigators will allegedly find out that he had recently met with Osama bin Laden. Later in 2003, authors Nick Fielding and Yosri Fouda will claim that not long after KSM is transferred from Pakistani to US custody, he confesses that he had met with bin Laden within the past two months. Bin Laden is said to be in good health. KSM met him in the Pakistani province of Baluchistan after a journey involving a complicated network of phone calls and couriers. He also says that bin Laden has been concentrating his forces in South Waziristan, in Pakistan’s tribal region, and bin Laden has formed an alliance with Afghan warlord Gulbuddin Hekmatyar. Fielding and Fouda will note that this story seems confirmed by the fact that within days of KSM’s arrest, residents in the town of Chaman in Baluchistan said that US aircraft dropped millions of leaflets mentioning the $25 million reward for bin Laden’s arrest. KSM also allegedly claims to know that al-Qaeda second-in-command Ayman al-Zawahiri recently returned to Quetta, Pakistan, after spending time in the Middle East. Also within days of KSM’s arrest, millions of leaflets about al-Zawahiri and his reward are dropped in that region. [Fouda and Fielding, 2003, pp. 184] It is likely that KSM is tortured during this time (see Shortly After February 29 or March 1, 2003). KSM will later say, “During the harshest period of my interrogation, I gave a lot of false information in order to satisfy what I believed the interrogators wished to hear in order to make the ill-treatment stop” (see March 7 – Mid-April, 2003).
February-Late March 2003: US Intelligence Learns Al-Qaeda Called Off Chemical Bomb Attack in US, but Effectiveness of Bomb is Disputed
In February 2003, some radical militants are arrested in Bahrain. A joint US-Saudi raid of an apartment in Saudi Arabia owned by one of them reveals the designs for a bomb called a mubtakkar. This bomb is made of two widely available chemicals, sodium cyanide and hydrogen, which combine to create hydrogen cyanide. When turned to gas, it is lethal, and counterterrorism experts are highly alarmed at this technical breakthrough. CIA Director Tenet briefs President Bush about the mubtakkar bomb in early March. [Suskind, 2006, pp. 193-197; Time, 6/17/2006] Journalist Ron Suskind calls it a “nightmare delivery system—portable, easy to construct, deadly.” The CIA has a highly placed al-Qaeda informant codenamed Ali, and in late March they contact him to learn more about the bomb. He tells his CIA handlers that Yusef al-Ayeri, a Saudi in charge of al-Qaeda operations in the Arabian peninsula, visited al-Qaeda number two leader Ayman al-Zawahiri in January 2003. He told al-Zawahiri of an already advanced plot in the US. Operatives loosely linked to al-Qaeda had traveled to the US in the fall of 2002 and thoroughly cased locations in New York City. They would place the mubtakkar bomb in subway cars and remotely activate them. The group was ready to implement an attack in about 45 days. According to Suskind, several thousand people could be killed. But Ali learned that al-Zawahiri called off the attacks, though Ali does not know the reason why. The group did cancel the attack, and US intelligence never learns who exactly they were. President Bush and others puzzle why the attack was canceled and speculate that al-Qaeda put it aside in favor of an even bigger attack. [Suskind, 2006, pp. 216-220; Time, 6/17/2006] Suskind’s account will cause alarm when revealed in 2006. Sen. Charles Schumer (D-NY) will say that authorities took the plot seriously but were never able to confirm its existence. Other officials will debate the effectiveness of the bomb and how many deaths it could have caused. [CNN, 6/18/2006] University of Maryland professor Milton Leitenberg later says of the bomb, “What you would get, in all probability, is a big bang, a big splash, but very little gas.” He also says that concentrations of key chemicals present in household materials are so low “you would get next to nothing” by using them, and one would have to get them from a chemical supplier or steal them from a laboratory. One counterterrorism official points out, “If this is such an amazing weapon, and the design for it is out there, why has no one ever used it?” [United Press International, 6/27/2006] An article by the private intelligence service Stratfor is also skeptical and suggests that al-Zawahiri called off the attack because it wouldn’t have been as deadly as if conventional bombs were used instead. [Stratfor, 6/21/2006] CIA Deputy Counter Terrorism Center Director Hank Crumpton will also later suggest that a team was recruited to stage the attack but apparently never was sent to the US. [Newsweek, 8/28/2007]
September 28, 2003: Al-Zawahiri Apparently Calls for Overthrow of Pakistani President Musharraf
A man thought to be al-Qaeda second-in-command Ayman al-Zawahiri calls for the overthrow of Pakistani President Pervez Musharraf in an audio cassette made public on this day. The man calls on Pakistanis to “unite and cooperate to topple this traitor and install a sincere leadership that would defend Islam and Muslims.” [Rashid, 2008, pp. 230, 436] There will be two apparently al-Qaeda-linked assassination attempts against Musharraf in December 2003 (see December 14 and 25, 2003).
December 14 and 25, 2003: Pakistani President Musharraf Survives Two Al-Qaeda-Linked Assassination Attempts
On December 14, 2003, Pakistani President Pervez Musharraf survives an assassination attempt when a powerful bomb goes off 30 seconds after his highly-guarded convoy crosses a bridge in Rawalpindi, Pakistan. The heavily guarded bridge is just a mile from Musharraf’s house, yet militants were able to spend severals days tying explosives to the pylons below it. His life is saved by a jamming device in his car given to him by the FBI, which temporarily jams all telephone signals and thus delays the explosion. On December 25, 2003, two suicide bombers launch another attempt to assassinate Musharraf, driving car bombs into his convoy a short distance from the location of the previous attack. Their car bombs fail to kill him and he escapes with only a cracked windscreen on his car, but 16 others nearby are killed.
Investigation – The identities of the two suicide bombers are soon discovered. One is Mohammed Jamil, a member of the Jaish-e-Mohammed (JEM) militant group who fought with the Taliban. The other is Hazir Sultan, who also fought with the Taliban. The memory chip from Jamil’s phone is found in the debris, and it is discovered he talked to a policeman who told him the timing of Musharraf’s convoy. Only a handful of military officers knew the route and timing of Musharraf’s travels and which of several identical cars he would be using at any given time, suggesting that elements within the military were involved in the attacks. Investigators also discover that the explosives used in the attacks came from an al-Qaeda camp in the Pakistani tribal area of South Waziristan. [Rashid, 2008, pp. 230-232]
Militant Leaders against Musharraf – Osama bin Laden apparently called for Musharraf’s overthrow in October 2002 (see October 9, 2002), and Ayman al-Zawahiri apparently did the same in September 2003 (see September 28, 2003). In the months prior to the assassination attempts, Maulana Masood Azhar, head of JEM, gave a speech at a prominent mosque calling for Musharraf’s assassination. [BBC, 7/27/2007]
Limited Crackdown – Musharraf responds by reshuffling positions in the military high command. More than 150 military and security personnel will eventually be arrested and interrogated. Twelve suspects are eventually found guilty and sentenced to death for roles in the attacks; at least six are military officers. It is believed the suicide bombers and these officers were recruited and trained by Amjad Farooqi, a JEM leader also closely linked to al-Qaeda and the Taliban. Al-Qaeda leader Abu Faraj al-Libbi, said to be Farooqi’s superior, is also allegedly involved. A massive manhunt for Farooqi and al-Libbi will ensue. Farooqi will eventually be killed in September 2004 (see September 27, 2004) and al-Libbi captured in May 2005 and taken into US custody (see May 2, 2005). However, Musharraf’s response is relatively restrained. He avoids calls to launch a crackdown on the entire Islamist militant movement in Pakistan. He does not ban any militant groups, nor does he arrest militant leaders, not even Azhar, the head of JEM who had publicly called for his assassination. (JEM had been banned in Pakistan for a second time the month before (see November 2003).) He does allow the Pakistani Army to attack the safe haven of South Waziristan several months later, but only after the US gives him an ultimatum, essentially forcing him to do so (see March 18- April 24, 2004). [BBC, 9/27/2004; Rashid, 2008, pp. 230-232]
January 2004: US Not Advertising Reward Program in Pakistan Where Most Al-Qaeda Leaders Are Hiding; Program Not Fixed Later
In 2004, Rep. Mark Steven Kirk (R-Ill) visits Pakistan to find out why the US Rewards for Justice program has generated so little information regarding al-Qaeda’s leadership. In the early 1990s, the program was effective in helping to catch al-Qaeda bomber Ramzi Yousef after a $2 million reward was announced for him and a huge number of matchboxes with his picture and the reward information on it were distributed in countries where he was likely to be (see April 2, 1993). The program has $25 million rewards for al-Qaeda leaders Osama bin Laden and Ayman al-Zawahiri, and lesser rewards for other al-Qaeda leaders. Kirk discovers that the US Embassy in Islamabad, Pakistan has effectively shut down the reward program. There is no radio or television advertising. A bin Laden matchbook campaign had begun in 2000 (see February 16, 2000), but the embassy has stopped giving away matchbooks with photos of bin Laden and other leaders. Kirk will later say: “We were at zero. I couldn’t believe it.” Embassy officials tell Kirk they are busy with other issues, such as assisting US troops in Afghanistan. Kirk proposes a congressional bill that would increase funding for the rewards program to advertise, extend the program to target drug kingpins (especially those who fund al-Qaeda and the Taliban), and make other reforms and improvements. But apparently the bill does not pass and the problem is not fixed. In 2008, Kirk will complain, “[T]he key thing about the Rewards for Justice program is that no one in a rural area—anywhere—knows about it.” Former CIA officer Arthur Keller will also say in 2008 that there are people in Pakistan and elsewhere with information who would be open to informing. “They’d love to have a $25 million bounty, and they aren’t supportive of Osama. But they don’t necessarily trust the US. Who do you report it to? The local police chief?… They’re not sure who to turn to or who to trust.” [US Congress, House, 2/12/2004; Washington Post, 5/17/2008] In 2006, the program will conduct a large advertising blitz in the US, seemingly one of the most unlikely places to figure leaders such as bin Laden (see December 2006).
March 18- April 24, 2004: Pakistani Army Offensive Fails to Defeat Al-Qaeda in Border Safe Haven
In mid-March 2004, Secretary of State Colin Powell visits Pakistan. He reportedly gives Pakistani President Pervez Musharraf an ultimatum: either Pakistan attacks the al-Qaeda safe haven in the South Waziristan tribal region, or the US will. On March 16, hundreds of Frontier Corps soldiers surround a compound in the village of Kalosha, a few miles from the capital of South Waziristan. Apparently, they are looking for Tahir Yuldashev, the leader of the Islamic Movement of Uzbekistan (IMU), an al-Qaeda-linked militant group based in nearby Uzbekistan. But the poorly trained Frontier Corps local militia have walked into a trap, and are badly defeated by about 2,000 al-Qaeda, Taliban, and IMU militants who greatly outnumber them. Yuldashev escapes.
Escalation – Ali Jan Orakzai, the regional commander of the Pakistani army, immediately rushes in eight thousand regular troops in an effort to save the situation. For the next two weeks, heavy fighting rages in South Waziristan. Helicopter gunships, fighter bombers, and heavy artillery are brought in to help defeat the militants, but the militants have heavy weapons as well and command the heights in extremely difficult mountainous terrain. [Rashid, 2008, pp. 270-271]
Al-Zawahiri Supposedly Surrounded – On March 18, Musharraf boasts on CNN that a “high-value target” has been surrounded, and suggests that it could be al-Qaeda second-in-command Ayman al-Zawahiri. He claims that 200 well-armed al-Qaeda fighters are protecting him. [CNN, 3/18/2004; FOX News, 3/18/2004] On March 19, Pakistani officials say that al-Zawahiri has escaped the South Waziristan village where he was supposedly surrounded. [Interactive Investor, 3/19/2004] In all likelihood, al-Zawahiri was never there, but was used as an excuse to justify the debacle.
Al-Qaeda Victorious – Heavy fighting continues for the next several weeks. Musharraf eventually orders local commanders to strike a deal with the militants to end the fighting. The fighting finally ends on April 24, when the Pakistani government signs an agreement with the militants, pardoning their leaders. The government claims that 46 of its soldiers were killed, while 63 militants were killed and another 166 were captured. But privately, army officers admit that their losses were close to 200 soldiers killed. US officials monitoring the fighting will later admit that the army attack was a disaster, resulting from poor planning and a near total lack of coordination. Pakistani journalist and regional expert Ahmed Rashid will later comment: “But there were deeper suspicions. The ISI had held meetings with the militants and possessed detailed information about the enemy’s numbers and armaments, but this intelligence did not seem to have been conveyed to the Frontier Corps. Western officers in [Afghanistan and Pakistan] wondered if the failed attack was due to a lack of coordination or was deliberate.” Orakzai, the army commander in charge of the offensive, reportedly intensely hates the US and has sympathy for the Taliban (see Late 2002-Late 2003). But there is no internal inquiry, even though many soldiers deserted or refused to fire on the militants. Nek Mohammed, a native local militant leader, emerges as a hero (see April 24-June 18, 2004). [PBS Frontline, 10/3/2006; Rashid, 2008, pp. 270-271]
July 8, 2004: Magazine Correctly Predicts ‘July Surprise’ Al-Qaeda Arrest
On July 8, 2004, the New Republic predicts a “July surprise” from the Bush-Cheney reelection campaign involving the arrest of a high-value target in Pakistan by the end of the month. The magazine reports that in the spring of 2004, the administration increased pressure on Pakistan to kill or capture Osama bin Laden, his deputy, Ayman al-Zawahiri, or Taliban leader Mullah Mohammed Omar, all believed to be hiding in Pakistan. Bush officials such as CIA Director George Tenet, Secretary of State Colin Powell and his assistant, Christina Rocca, State Department counterterrorism chief Cofer Black, and others all visited Pakistan in recent months to urge Pakistan to increase its efforts in the war on terrorism. The New Republic comments, “This public pressure would be appropriate, even laudable, had it not been accompanied by an unseemly private insistence that the Pakistanis deliver these high-value targets (HVTs) before Americans go to the polls in November.” Bush spokespeople deny that the administration exerted any such pressure. But according to one source in the Pakistani ISI, “The Pakistani government is really desperate and wants to flush out bin Laden and his associates after the latest pressures from the US administration to deliver before the [upcoming] US elections.” Another source in the Pakistani Interior Ministry says, “The Musharraf government has a history of rescuing the Bush administration. They now want Musharraf to bail them out when they are facing hard times in the coming elections.” And another ISI source says that the Pakistanis “have been told at every level that apprehension or killing of HVTs before [the] election is [an] absolute must.” The Pakistanis have even been given a target date, according to the second ISI source: “The last ten days of July deadline has been given repeatedly by visitors to Islamabad and during [ISI director Lieutenant General Ehsan ul-Haq’s] meetings in Washington.” The source says that a White House aide told ul-Haq last spring that “it would be best if the arrest or killing of [any] HVT were announced on twenty-six, twenty-seven, or twenty-eight July”—the first three days of the Democratic National Convention in Boston. One Pakistani general said recently, “If we don’t find these guys by the election, they are going to stick this whole nuclear mess [relating to A. Q. Khan] up our _sshole.” The Bush administration apparently is using a carrot-and-stick approach to make sure such an arrest takes place on schedule. The New Republic observes: “Pushing Musharraf to go after al-Qaeda in the tribal areas may be a good idea despite the risks. But, if that is the case, it was a good idea in 2002 and 2003. Why the switch now? Top Pakistanis think they know: This year, the president’s reelection is at stake.” [New Republic, 7/29/2004] Pakistan will announce the capture of al-Qaeda leader Ahmed Khalfan Ghailani on July 29, just hours before Democratic presidential John Kerry’s acceptance speech at the Democratic National Convention. The authors of the New Republic article will claim vindication for their prediction (see July 25-29, 2004).
