In September, Osama bin Laden and 15 other Islamists form the group al-Qaida, or "the base", to continue their jihad, or holy war, against the Soviets and other who they say oppose their goal of a pure nation governed by Islam. With their belief that the Soviet's faltering war in Afghanistan was directly attributable to their fighting, they claim victory in their first battle, but also begin to shift their focus to America, saying the remaining superpower is the main obstacle to the establishment of a state based on Islam.

The U.S., Pakistan, Afghanistan, and the Soviet Union sign peace accords in Geneva guaranteeing Afghan independence and the withdrawal of 100,000 Soviet troops. Following Soviet withdrawal, the Mujahadeen continue their resistance against the Soviet-backed regime of communist president Dr. Mohammad Najibullah, who had been elected president of the puppet Soviet state in 1986. Afghan guerrillas name Sibhatullah Mojadidi as head of their exiled government.

The Mujahadeen and other rebel groups, with the aid of turncoat government troops, storm the capital, Kabul, and oust Najibullah from power. Ahmad Shah Masood, legendary guerrilla leader, leads the troops into the capital. The United Nations offers protection to Najibullah. The Mujahadeen, a group already beginning to fracture as warlords fight over the future of Afghanistan, form a largely Islamic state with professor Burhannudin Rabbani as president.