Despite the public pledge of support, Pakistan was widely believed by both international observers and the subsequent Afghan government alike to maintain their backing of Taliban and, in the view of some, al-Qaeda.

Pakistan's motivations for covert activities in Afghanistan, since the cessation of hostilities between the two nations in the mid-1970s, have largely focused on supporting (Hezb-i Islami, Taliban) or opposing (PDPA, Soviet, Northern Alliance) various groups in an attempt to dictate the Afghan government in Kabul.

This program to seat and preserve an Afghan government friendly to Pakistani (and intrinsically anti-Indian) interests has largely centered on support to groups ideologically aligned with Islamabad, typically Pashtun, socially conservative, political Islamist, and Deobandi (Sunni).

[6] In a polemical assessment, Afghan feminist Alia Rawi Akbar writes that Massoud, during this uprising, "by the order of ISI", assassinated the mayor "of his home city", before he "ran to Pakistan.

"[7] Another historian of the ISI, Owen Sirrs, specifies how the 1973 coup d'état which brought president Sardar Mohammed Daoud Khan to power, a proponent of a Pashtunistan independent state and fiercely anti-Pakistan, helping both Pashtun and Baloch militants, convinced Bhutto to use Islamist rebels in order to fight the ethnic Pashtun or Baloch brands of nationalism, and he described the ISI plan in multiple phases, "phase one was stepping up intelligence collection in that country, including ferreting out potential Afghan allies and weaknesses in the Daoud regime.

Phase three involved joint anti-Afghan operations with Iran, since both the Shah and Bhutto regarded the PDPA as a threat to the regional balance of power.

Iran’s intelligence service, SAVAK, backed several anti-Daoud groups unilaterally, but ISI wanted to entice the Iranians into joint missions against the Afghans.

The last phase in ISI’s game plan was also the most important: recruiting an insurgent army from the growing number of anti-Daoud Afghan exiles in Pakistan."

These insurgents would include the likes of Ahmed Shah Massoud, Burhanuddin Rabbani, Sibghatullah Mojadeddi, Gulbuddin Hekmatyar, Jalaleddin Haqqani and Abd al-Rasul Sayyaf, all future political heavyweights of the country.

"[9] Abdullah Anas, the leading Afghan Arab and also their key ideologue, in his memoirs says that ISI supported the Tajiks insurgents "with the blessing of Pakistan's president Zulfikar Ali Bhutto who hoped to use this uprising as a means to pressurise the Afghan government to resolve the border disputes over Baluchistan and Pashtunistan", while describing their first military insurrection, in 1975, as "a fiasco" : Hekmatyar, who remained in Peshawar, sent men to attack government outposts in Surkhrud, without much success, while a second group, led by Massoud, in his native Panjshir valley, took control of government buildings for few days before eventually losing them, as well as many of his men, to Daud Khan's forces, something which irritated him and made him wary of Hekmatyar, blaming him for the failed operation.

[21] Afghanistan expert Amin Saikal concludes in Modern Afghanistan: A History of Struggle and Survival: Pakistan was keen to gear up for a breakthrough in Central Asia.... Islamabad could not possibly expect the new Islamic government leaders... to subordinate their own nationalist objectives in order to help Pakistan realize its regional ambitions.... Had it not been for the ISI's logistic support and supply of a large number of rockets, Hekmatyar's forces would not have been able to target and destroy half of Kabul.

"[24] Al-Jazeera wrote in early 2012 that Presidential Chief of Staff, Karim Khoram from Hekmatyar's Hezb-e Islami, besides controlling the Government Media and Information Center, enjoyed a "tight grip" over President Karzai.

"[25] Senior non-Hezb-e Islami Pashtun officials in the Afghan government accused Khoram of acting as a spy for Pakistan's Inter-Services Intelligence.

[34] William Maley, Professor at the Australian National University and Director of the Asia-Pacific College, writes on the emergence of the Taliban in Afghanistan: "In 1994, with the failure of [Gulbuddin Hekmatyar's alliance] attempt to oust [the Afghan] Rabbani [administration], Pakistan found itself in an awkward position.

... On 29 October 1994, a convoy of trucks, including a notorious ISI officer, Sultan Amir ... and two figures who were later to become prominent Taliban leaders, entered Afghanistan.

The UN secretary-general criticized Pakistan for its military support and the Security Council stated it was "deeply distress[ed] over reports of involvement in the fighting, on the Taliban side, of thousands of non-Afghan nationals.

"[56] In June 2008, Afghan officials accused Pakistan's intelligence service of plotting a failed assassination attempt on President Hamid Karzai; shortly thereafter, they implied the ISI's involvement in a July 2008 Taliban attack on the Indian embassy.

Gates and others suggest the ISI maintains links with groups like the Afghan Taliban as a "strategic hedge" to help Islamabad gain influence in Kabul once U.S. troops exit the region.

[56] U.S. Chairman of the Joint Chiefs of Staff Admiral Mike Mullen in 2011 called the Haqqani network (the Afghan Taliban's most destructive element) a "veritable arm of Pakistan's ISI".

Amrullah Saleh, director of Afghanistan's intelligence service until June 2010, told Reuters in 2010 that the ISI was "part of a landscape of destruction in this country".

[59] In March 2012, the Commander of NATO forces in Afghanistan, General John Allen, told the United States Senate that as of 2012 there was still no change in Pakistan's policy of support for the Afghan Taliban and its Haqqani network.

[62] According to an investigative report among Afghan refugees inside Pakistan by The New York Times, people testified that "dozens of families had lost sons in Afghanistan as suicide bombers and fighters" and "families whose sons had died as suicide bombers in Afghanistan said they were afraid to talk about the deaths because of pressure from Pakistani intelligence agents, the ISI.

One former Taliban commander told The New York Times that such arrests were then sold to the Westerners and others as part of a supposed Pakistani collaboration effort in the War against Terror.

[65] Gen. James L. Jones, then NATO's supreme commander, in September 2007 testified in front of the U.S. Senate Foreign Relations Committee that the Afghan Taliban movement uses the Pakistani city of Quetta as their main headquarters.

[68] U.S. Chairman of the Joint Chiefs of Staff Admiral Mike Mullen in 2011 called the Haqqani network (the Afghan Taliban's most destructive element) a "veritable arm of Pakistan's ISI".

[77] Bin Laden sent Arab and Central Asian Al-Qaeda militants to join the Taliban's and Pakistan's fight against the United Front (Northern Alliance) among them his Brigade 055.

[79] In 2007, the Afghans specifically identified two Al-Qaeda safe houses in Manshera, a town just miles from Abbottabad, leading them to believe that Bin Laden was possibly hiding there.

'"[79] A December 2011 analysis report by the Jamestown Foundation comes to the conclusion that "in spite of denials by the Pakistani military, evidence is emerging that elements within the Pakistani military harbored Osama bin Laden with the knowledge of former army chief General Pervez Musharraf and possibly current Chief of Army Staff (COAS) General Ashfaq Pervez Kayani.

The ISI has also been accused of having been involved in the murder of former Afghan president and chief of the Karzai's administration High Peace Council Burhanuddin Rabbani and several other anti-Taliban leaders.

"[17] Consequently, neither Massoud nor Abdul Haq were consulted before and neither participated in the Battle of Jalalabad (1989) in which the ISI tried but failed to install Gulbuddin Hekmatyar as the post-communist leader of Afghanistan.