Hamid Karzai first became involved in the mujahidin government of Burhanuddin Rabbani, serving as deputy foreign minister from 1992 to 1994. As was the case during the 1980s, the government in those years was immobilized by ethnic infighting. When the Taliban took control of Kabul 27 September 1996, Karzai initially supported them; in fact, the Taliban government unsuccessfully tried to name him as their ambassador to the UN, but the UN did not recognize the Taliban's right to Afghanistan's seat. Karzai and his father, growing suspicious that the Taliban was being controlled by foreign influences, broke with the Taliban and began to criticize the religious movement while in exile in Quetta, Pakistan. When Karzai's father was assassinated in 1999 as he walked home from a mosque, most in the government and in international organizations attributed the act to members of the Taliban.
Following his father's death, Karzai became leader of the Popolzai clan from his exile post in Quetta. He and his followers continued to campaign against the repressive Taliban regime, but they received little international attention or support. Karzai frequently traveled to the United States from Quetta to lobby for support to overthrow the Taliban. His visits included stops at the University of Nebraska where the faculty includes experts on Afghanistan; in 2001 Karzai testified before the U.S. Senate Foreign Relations Committee. When the 11 September 2001 terrorist attacks against the United States brought Afghanistan to the center of international attention, U.S. government officials began to listen more seriously to Karzai's ideas. In October, Karzai secretly entered Afghanistan in an attempt to build support for a plan to oust the Taliban and to convene a loya jirga (council of elders) to install a new government.
In 2001, after the Taliban government crumbled, the UN convened a meeting in Bonn, Germany, of four Afghan factions to begin to build a coalition government to lead the country in its next stage of rebuilding. All factions agreed to name Hamid Karzai as chairman of the interim administration; in addition, the factions agreed that the popular former king, Mohammed Zahir Shah, should return to Afghanistan (from Italy, where he had been living in exile) to play a symbolic role in the next administration. At a separate meeting at the same time, representatives of UN member nations were considering funding and other issues of support for Afghanistan.
The loya jirga met from 11–19 June 2002 and Karzai was elected president of the Transitional Authority. The meeting of the loya jirga highlighted the power of faction leaders from the mainly Tajik former Northern Alliance, who were influential in assuring Karzai's election.