Inter-Services Intelligence activities in Afghanistan

The Inter-Services Intelligence (ISI) intelligence agency of Pakistan has been accused of being heavily involved in covertly running military intelligence programs in Afghanistan since before the Soviet invasion of Afghanistan in 1979. The first ISI operation in Afghanistan took place in 1975. It was in "retaliation to Republic of Afghanistan's proxy war and support to the militants against Pakistan". Before 1975, ISI did not conduct any operation in Afghanistan and it was only after decade of Republic of Afghanistan's proxy war against Pakistan, support to militants and armed incursion in 1960 and 1961 in Bajaur that Pakistan was forced to retaliate. Later on, in the 1980s, the ISI in Operation Cyclone systematically coordinated the distribution of arms and financial means provided by the United States Central Intelligence Agency (CIA) to factions of the Afghan mujahideen such as the Hezb-e Islami (HeI) of Gulbuddin Hekmatyar and the forces of Ahmad Shah Massoud whose forces would later be known as the Northern Alliance. After the Soviet retreat, the different Mujahideen factions turned on each other and were unable to come to a power sharing deal which resulted in a civil war. The United States, along with the ISI and the Pakistani government of Prime Minister Benazir Bhutto became the primary source of support for Hekmatyar in his 1992–1994 bombardment campaign against the Islamic State of Afghanistan and the capital Kabul.

It is widely agreed that after Hekmatyar failed to take over power in Afghanistan. The ISI and other parts of the Pakistan military subsequently provided financial, logistical, military and direct combat support to the Taliban until the September 11 attacks of 2001. It is widely acknowledged that the ISI has given the Afghan Taliban safe havens inside Pakistan and supported the Taliban's resurgence in Afghanistan after 9/11 helping them, especially the Haqqani network, carry out attacks inside Afghanistan. Pakistani officials deny this accusation. Allegations have been raised by international government officials, policy analysts and even Pakistani military officials that the ISI in conjunction with the military leadership has also provided some amount of support and refuge to al-Qaeda. Such allegations were increasingly issued when Al-Qaeda leader Osama bin Laden was killed in 2011 while living in the Pakistani city of Abbottabad.