After the fall of Kabul to the Taliban on September 27, 1996, Ahmad Shah Massoud and Abdul Rashid Dostum, two former archnemesis, created the United Front (Northern Alliance) against the Taliban that were preparing offensives against the remaining areas under the control of Massoud and those under the control of Dostum. According to Human Rights Watch, in late May 1997, some 3,000 captive Taliban soldiers were summarily executed in and around Mazar-i-Sharif by Dostum's Junbish forces and members of the Shia Hazara Hezb-i Wahdat faction. The Taliban defeated Dostum's Junbish forces militarily by seizing Mazar-i-Sharif in 1998. Dostum went into exile.
Former Pakistani President Pervez Musharraf sent more troops against the United Front of Ahmad Shah Massoud than the Afghan Taliban. According to the United Nations, the Taliban, while trying to consolidate control over northern and western Afghanistan, committed systematic massacres against civilians. U.N. officials stated that there had been "15 massacres" between 1996 and 2001. These have been highly systematic and they all lead back to the Taliban Ministry of Defense or to Mullah Omar himself." The Taliban especially targeted people of Shia religious or Hazara ethnic background. Upon taking Mazar-i-Sharif in 1998, about 4,000 civilians were executed by the Taliban and many more reported tortured. The documents also reveal the role of Arab and Pakistani support troops in these killings. Bin Laden's so-called 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.
Pakistani President Pervez Musharraf - then as Chief of Army Staff - was responsible for sending thousands of Pakistanis to fight alongside the Taliban and Bin Laden against the forces of Massoud. In total there were believed to be 28,000 Pakistani nationals fighting inside Afghanistan. About 20,000 were regular Pakistani soldiers either from the Frontier Corps or army and an estimated 8,000 were militants recruited in madrassas filling regular Taliban ranks. The estimated 25,000 Taliban regular force thus comprised more than 8,000 Pakistani nationals. A 1998 document by the U.S. State Department confirms that "20-40 percent of Taliban soldiers are Pakistani." The document further states that the parents of those Pakistani nationals "know nothing regarding their child's military involvement with the Taliban until their bodies brought back to Pakistan." Further 3,000 fighters of the regular Taliban army were Arab and Central Asian militants. From 1996 to 2001 the Al Qaeda of Osama Bin Laden and Ayman al-Zawahiri became a state within the Taliban state. Bin Laden sent Arab recruits to join the fight against the United Front. Of roughly 45,000 Pakistani, Taliban and Al Qaeda soldiers fighting against the forces of Massoud only 14,000 were Afghan.
Ahmad Shah Massoud remained 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. Human Rights Watch cites no human rights crimes for the forces under direct control of Massoud for the period from October 1996 until the assassination of Massoud in September 2001. As a consequence many civilians fled to the area of Ahmad Shah Massoud. In total, estimates range up to one million people fleeing the Taliban. In early 2001 Massoud addressed the European Parliament in Brussels asking the international community to provide humanitarian help to the people of Afghanistan. He stated that the Taliban and Al Qaeda had introduced "a very wrong perception of Islam" and that without the support of Pakistan and Bin Laden the Taliban would not be able to sustain their military campaign for up to a year. On this visit to Europe he also warned that his intelligence had gathered information about a large-scale attack on U.S. soil being imminent.
On September 9, 2001, Ahmad Shah Massoud died in a suicide attack by two Arab suicide bombers in the Afghan province of Takhar. Two days later 3,000 people died on U.S. soil in the attacks of September 11, 2001. Following the September 11, 2001 attacks the U.S. government identified Osama Bin Laden alongside Khalid Sheikh Mohammed as the faces behind the attacks. When the Taliban refused to hand over Osama Bin Laden to U.S. authorities and refused to disband Al Qaeda bases in Afghanistan, the U.S. and British air forces began bombing al-Qaeda and Taliban targets inside Afghanistan during Operation Enduring Freedom. On the ground, American and British special forces along with CIA Special Activities Division units worked with commanders of the United Front (Northern Alliance) to launch a military offensive against the Taliban forces. These attacks led to the fall of Mazar-i-Sharif and Kabul in November 2001, as the Taliban and al-Qaida retreated toward the mountainous Durand Line border with Pakistan. In December 2001, after the Taliban government was toppled and the new Afghan government under Hamid Karzai was formed, the International Security Assistance Force (ISAF) was established by the UN Security Council to help assist the Karzai administration and provide basic security to the Afghan people.