Before the start of war
Origins of Afghanistan's civil war
Afghanistan's political order began to break down with the overthrow of King Zahir Shah by his distant cousin Mohammed Daoud Khan in a bloodless 1973 Afghan coup d'état. Daoud Khan had served as prime minister since 1953 and promoted economic modernization, emancipation of women, and Pashtun nationalism. This was threatening to neighboring Pakistan, faced with its own restive Pashtun population. In the mid-1970s, Pakistani Prime Minister Zulfikar Ali Bhutto began to encourage Afghan Islamist leaders such as Burhanuddin Rabbani and Gulbuddin Hekmatyar, to fight against the regime. In 1978, Daoud Khan was killed in a coup by Afghan's Communist Party, his former partner in government, known as the People's Democratic Party of Afghanistan (PDPA). The PDPA pushed for a socialist transformation by abolishing arranged marriages, promoting mass literacy and reforming land ownership. This undermined the traditional tribal order and provoked opposition across rural areas. The PDPA's crackdown was met with open rebellion, including Ismail Khan's Herat Uprising. The PDPA was beset by internal leadership differences and was weakened by an internal coup on 11 September 1979 when Hafizullah Amin ousted Nur Muhammad Taraki. The Soviet Union, sensing PDPA weakness, intervened militarily three months later, to depose Amin and install another PDA faction led by Babrak Karmal.
The entry of Soviet forces in Afghanistan in December 1979 prompted its Cold War rivals, the United States, Pakistan, Saudi Arabia and China to support rebels fighting against the Soviet-backed Democratic Republic of Afghanistan. In contrast to the secular and socialist government, which controlled the cities, religiously motivated mujahideen held sway in much of the countryside. Beside Rabbani, Hekmatyar, and Khan, other mujahideen commanders included Jalaluddin Haqqani. The CIA worked closely with Pakistan's Inter-Service Intelligence to funnel foreign support for the mujahideen. The war also attracted Arab volunteers, known as "Afghan Arabs", including Osama bin Laden.
After the withdrawal of the Soviet military from Afghanistan in May 1989, the PDPA regime under Najibullah held on until 1992, when the collapse of the Soviet Union deprived the regime of aid, and the defection of Uzbek general Abdul Rashid Dostum cleared the approach to Kabul. With the political stage cleared of socialists, the warlords, some of them Islamist, vied for power. By then, Bin Laden had left the country and the United States' interest in Afghanistan also diminished.
Warlord rule (1992–1996)
In 1992, Rabbani officially became president of the Islamic State of Afghanistan, but had to battle other warlords for control of Kabul. In late 1994, Rabbani's defense minister, Ahmad Shah Massoud, defeated Hekmatyar in Kabul and ended ongoing bombardment of the capital. Massoud tried to initiate a nationwide political process with the goal of national consolidation. Other warlords, including Ismail Khan in the west and Dostum in the north, maintained their fiefdoms.
In 1994, Mohammed Omar, a mujahideen member who taught at a Pakistani madrassa, returned to Kandahar and formed the Taliban movement. His followers were religious students, known as the Talib and they sought to end warlordism through strict adherence to Islamic law. By November 1994, the Taliban had captured all of Kandahar Province. They declined the government's offer to join in a coalition government and marched on Kabul in 1995.
Taliban Emirate vs Northern Alliance
The Taliban's early victories in 1994 were followed by a series of costly defeats. Pakistan provided strong support to the Taliban. Analysts such as Amin Saikal described the group as developing into a proxy force for Pakistan's regional interests, which the Taliban denied. The Taliban started shelling Kabul in early 1995, but were driven back by Massoud.
On 27 September 1996, the Taliban, with military support by Pakistan and financial support from Saudi Arabia, seized Kabul and founded the Islamic Emirate of Afghanistan. They imposed their fundamentalist interpretation of Islam in areas under their control, issuing edicts forbidding women to work outside the home, attend school, or to leave their homes unless accompanied by a male relative. According to the Pakistani expert Ahmed Rashid, "between 1994 and 1999, an estimated 80,000 to 100,000 Pakistanis trained and fought in Afghanistan" on the side of the Taliban.
Massoud and Dostum, former arch-enemies, created a United Front against the Taliban, commonly known as the Northern Alliance. In addition to Massoud's Tajik force and Dostum's Uzbeks, the United Front included Hazara factions and Pashtun forces under the leadership of commanders such as Abdul Haq and Haji Abdul Qadir. Abdul Haq also gathered a limited number of defecting Pashtun Taliban. Both agreed to work together with the exiled Afghan king Zahir Shah. International officials who met with representatives of the new alliance, which the journalist Steve Coll referred to as the "grand Pashtun-Tajik alliance", said, "It's crazy that you have this today … Pashtuns, Tajiks, Uzbeks, Hazara … They were all ready to buy in to the process … to work under the king's banner for an ethnically balanced Afghanistan." The Northern Alliance received varying degrees of support from Russia, Iran, Tajikistan and India. The Taliban captured Mazar-i-Sharif in 1998 and drove Dostum into exile.
The conflict was brutal. According to the United Nations (UN), the Taliban, while trying to consolidate control over northern and western Afghanistan, committed systematic massacres against civilians. UN officials stated that there had been "15 massacres" between 1996 and 2001. The Taliban especially targeted the Shia Hazaras. In retaliation for the execution of 3,000 Taliban prisoners by Uzbek general Abdul Malik Pahlawan in 1997, the Taliban executed about 4,000 civilians after taking Mazar-i-Sharif in 1998.
Bin Laden's 055 Brigade was responsible for mass killings of Afghan civilians. The report by the United Nations quotes eyewitnesses in many villages describing "Arab fighters carrying long knives used for slitting throats and skinning people".
By 2001, the Taliban controlled as much as 90% of Afghanistan, with the Northern Alliance confined to the country's northeast corner. Fighting alongside Taliban forces were some 28,000–30,000 Pakistanis (usually also Pashtun) and 2,000–3,000 Al-Qaeda militants. Many of the Pakistanis were recruited from madrassas. A 1998 document by the U.S. State Department confirmed that "20–40 percent of [regular] Taliban soldiers are Pakistani." The document said that many of the parents of those Pakistani nationals "know nothing regarding their child's military involvement with the Taliban until their bodies are brought back to Pakistan". According to the U.S. State Department report and reports by Human Rights Watch, other Pakistani nationals fighting in Afghanistan were regular soldiers, especially from the Frontier Corps, but also from the Pakistani Army providing direct combat support.
In August 1996, Bin Laden was forced to leave Sudan and arrived in Jalalabad, Afghanistan. He had founded Al-Qaeda in the late 1980s to support the Mujahideen's war against the Soviets, but became disillusioned by infighting among warlords. He grew close to Mullah Omar and moved Al-Qaeda's operations to eastern Afghanistan.
The 9/11 Commission in the U.S. found that under the Taliban, al-Qaeda was able to use Afghanistan as a place to train and indoctrinate fighters, import weapons, coordinate with other jihadists, and plot terrorist actions. While al-Qaeda maintained its own camps in Afghanistan, it also supported training camps of other organizations. An estimated 10,000 to 20,000 men passed through these facilities before 9/11, most of whom were sent to fight for the Taliban against the United Front. A smaller number were inducted into al-Qaeda.
After the August 1998 U.S. Embassy bombings were linked to bin Laden, President Bill Clinton ordered missile strikes on militant training camps in Afghanistan. U.S. officials pressed the Taliban to surrender bin Laden. In 1999, the international community imposed sanctions on the Taliban, calling for bin Laden to be surrendered. The Taliban repeatedly rebuffed these demands.
Central Intelligence Agency (CIA) Special Activities Division paramilitary teams were active in Afghanistan in the 1990s in clandestine operations to locate and kill or capture Osama bin Laden. These teams planned several operations, but did not receive the order to proceed from President Clinton. Their efforts built relationships with Afghan leaders that proved essential in the 2001 invasion.
Change in U.S. policy toward Afghanistan
During the Clinton administration, the U.S. tended to favor Pakistan and until 1998–1999 had no clear policy toward Afghanistan. In 1997, for example, the U.S. State Department's Robin Raphel told Massoud to surrender to the Taliban. Massoud responded that, as long as he controlled an area the size of his hat, he would continue to defend it from the Taliban. Around the same time, top foreign policy officials in the Clinton administration flew to northern Afghanistan to try to persuade the United Front not to take advantage of a chance to make crucial gains against the Taliban. They insisted it was the time for a cease-fire and an arms embargo. At the time, Pakistan began a "Berlin-like airlift to resupply and re-equip the Taliban", financed with Saudi money.
U.S. policy toward Afghanistan changed after the 1998 U.S. embassy bombings. Subsequently, Osama bin Laden was indicted for his involvement in the embassy bombings. In 1999 both the U.S. and the United Nations enacted sanctions against the Taliban via United Nations Security Council Resolution 1267, which demanded the Taliban surrender Osama bin Laden for trial in the U.S. and close all terrorist bases in Afghanistan. The only collaboration between Massoud and the U.S. at the time was an effort with the CIA to trace bin Laden following the 1998 bombings. The U.S. and the European Union provided no support to Massoud for the fight against the Taliban.
By 2001 the change of policy sought by CIA officers who knew Massoud was underway. CIA lawyers, working with officers in the Near East Division and Counter-terrorist Center, began to draft a formal finding for President George W. Bush's signature, authorizing a covert action program in Afghanistan. It would be the first in a decade to seek to influence the course of the Afghan war in favor of Massoud. Richard A. Clarke, chair of the Counter-Terrorism Security Group under the Clinton administration, and later an official in the Bush administration, allegedly presented a plan to incoming Bush National Security Adviser Condoleezza Rice in January 2001.
A change in U.S. policy was effected in August 2001. The Bush administration agreed on a plan to start supporting Massoud. A meeting of top national security officials agreed that the Taliban would be presented with an ultimatum to hand over bin Laden and other al-Qaeda operatives. If the Taliban refused, the U.S. would provide covert military aid to anti-Taliban groups. If both those options failed, "the deputies agreed that the United States would seek to overthrow the Taliban regime through more direct action."
Northern Alliance on the eve of 9/11
Ahmad Shah Massoud was the only leader of the United Front in Afghanistan. In the areas under his control, Massoud set up democratic institutions and signed the Women's Rights Declaration. As a consequence, many civilians had fled to areas under his control. In total, estimates range up to one million people fleeing the Taliban.
In late 2000, Ahmad Shah Massoud, a Tajik nationalist and leader of the Northern Alliance, invited several other prominent Afghan tribal leaders to a jirga in northern Afghanistan "to settle political turmoil in Afghanistan". Among those in attendance were Pashtun nationalists, Abdul Haq and Hamid Karzai.
In early 2001, Massoud and several other Afghan leaders addressed the European Parliament in Brussels, asking the to provide humanitarian help. The Afghan envoy asserted that the Taliban and al-Qaeda had introduced "a very wrong perception of Islam" and that without the support of Pakistan and Osama bin Laden, the Taliban would not be able to sustain their military campaign for another year. Massoud warned that his intelligence had gathered information about an imminent, large-scale attack on U.S. soil.
On 9 September 2001, two French-speaking Algerians posing as journalists killed Massoud in a suicide attack in Takhar Province of Afghanistan. The two perpetrators were later alleged to be members of al-Qaeda. They were interviewing Massoud before detonating a bomb hidden in their video camera. Both of the alleged al-Qaeda men were subsequently killed by Massoud's guards.
11 September attacks
On the morning of 11 September 2001, a total of 19 Arab men—15 of whom were from Saudi Arabia—carried out four coordinated attacks in the United States. Four commercial passenger jet airliners were hijacked. The hijackers – members of al-Qaeda's Hamburg cell – intentionally crashed two of the airliners into the Twin Towers of the World Trade Center in New York City, killing everyone on board and more than 2,000 people in the buildings. Both buildings collapsed within two hours from damage related to the crashes, destroying nearby buildings and damaging others. The hijackers crashed a third airliner into the Pentagon in Arlington, Virginia, just outside Washington, D.C. The fourth plane crashed into a field near Shanksville, in rural Pennsylvania, after some of its passengers and flight crew attempted to retake control of the plane, which the hijackers had redirected toward Washington, D.C., to target the White House, or the U.S. Capitol. No one aboard the flights survived. According to the New York State Health Department, the death toll among responders including firefighters and police was 836 as of June 2009. Total deaths were 2,996, including the 19 hijackers.
U.S. ultimatum to Taliban
The Taliban publicly condemned the 11 September attacks. U.S. President George W. Bush issued an ultimatum to the Taliban to hand over Osama bin Laden, "close immediately every terrorist training camp, hand over every terrorist and their supporters, and give the United States full access to terrorist training camps for inspection." Osama bin Ladin was protected by the traditional Pashtun laws of hospitality. In the weeks ahead and at the beginning of the US and NATO invasion of Afghanistan, Taliban demanded evidence of bin Laden's guilt, and consequently offered to hand over Osama bin Laden. US President, George W. Bush, rejected the idea, citing policies such as "we do not negotiate with terrorists." Britain deputy prime minister, John Prescott, claimed the group expressions amount to an admission of guilt for the September 11 attacks.
After the US invasion, Taliban repeatedly requested for due diligence investigation and willingness to handover Osama to a third country for due prosecutions. US refused and continued bombardments of Kabul airport and other cities. Haji Abdul Kabir, the third most powerful figure in the ruling Taliban regime , told reporters: "If the Taliban is given evidence that Osama bin Laden is involved, we would be ready to hand him over to a third country."  At an October 15, 2001 meeting in Islamabad, Wakil Ahmed Muttawakil, the foreign minister of Afghanistan, offered to remove Osama bin Laden to the custody of the Organization of the Islamic Conference (OIC) to be tried for the 9/11 terror attacks. The OIC is a large organization of 57 member states. Muttawakil by this point had dropped the condition that the U.S. furnish evidence of Osama bin Laden's involvement in the 9/11 attacks as a precondition for the transfer of Osama bin Laden by Afghanistan to the OIC for trial.