Пәкістан Әскери Барлау қызметі

Military intelligence service of Pakistan

The Inter Services Intelligence (ISI; ) is the largest and best known component of the Pakistani intelligence community. It is responsible for gathering, processing, and analyzing any information from around the world that is deemed relevant to Pakistan's national security. The ISI reports to its director general and is primarily focused on providing intelligence to the Pakistani government. The ISI primarily consists of serving military officers drawn on secondment from the three service branches of the Pakistan Armed Forces: the Pakistan Army, Pakistan Navy, and Pakistan Air Force, hence the name "Inter Services"; the agency also recruits civilians. Since 1971, it has been formally headed by a serving three star general of the Pakistan Army, who is appointed by the Prime Minister of Pakistan on the recommendation of the Chief of Army Staff, who recommends three officers for the position. as of 2024, the ISI is headed by Nadeem Anjum, a lieutenant general. The ISI director general reports directly to both the prime minister and the Chief of Army Staff. The agency gained global recognition and fame in the 1980s when it backed the Afghan mujahideen against the Soviet Union during the Soviet–Afghan War in the former Democratic Republic of Afghanistan. Over the course of the conflict, the ISI worked in close coordination with the Central Intelligence Agency of the United States and the Secret Intelligence Service of the United Kingdom to run Operation Cyclone, a program to train and fund the mujahideen in Afghanistan with support from China, Saudi Arabia, and other Muslim nations. Following the dissolution of the Democratic Republic of Afghanistan in 1992, the ISI provided strategic support and intelligence to the Taliban against the Northern Alliance during the Afghan Civil War in the 1990s. The ISI has strong links with jihadist groups, particularly in Afghanistan and Kashmir. Its special warfare unit is the Covert Action Division. The Federal Bureau of Investigation (FBI), in their first ever open acknowledgement in 2011 in US Court, said that the Inter Services Intelligence (ISI) sponsors and oversees the insurgency in Kashmir by arming separatist militant groups. On 5 July 1977 through Operation Fair Play, the ISI began collecting intelligence on the Pakistan Communist Party and the Pakistan Peoples Party. The Soviet–Afghan War in the 1980s saw the enhancement of the ISI's covert operations. A special Afghanistan section known as the SS Directorate was created under the command of Brigadier Mohammed Yousaf to oversee day to day operations in Afghanistan. Officers from the ISI's Covert Action Division received training in the United States, and "many covert action experts of the CIA were attached to the ISI to guide it in its operations against Soviet troops by using the Afghan Mujahideen". Many analysts (mainly Indian and American) believe that the ISI provides support to militant groups, though others think these allegations remain unsubstantiated. The ISI has often been accused of playing a role in major terrorist attacks across India including militancy in Kashmir, the July 2006 Mumbai Train Bombings, the 2001 Indian Parliament attack, the 2006 Varanasi bombings, the August 2007 Hyderabad bombings, and the November 2008 Mumbai attacks. The ISI has been accused of supporting Taliban forces and recruiting and training mujahideen to fight in Afghanistan and Kashmir. Based on communication interceptions, US intelligence agencies concluded Pakistan's ISI was behind the attack on the Indian embassy in Kabul on 7 July 2008, a charge that the governments of India and Afghanistan had laid previously. It is believed to be aiding these organisations in eradicating perceived enemies or those opposed to their cause, including India, Russia, China, Israel, the United States, the United Kingdom, and other members of NATO. Satellite imagery from the Federal Bureau of Investigation suggest the existence of several terrorist camps in Pakistan, with at least one militant admitting to being trained in the country. As part of the ongoing Kashmir conflict, Pakistan is alleged to be backing separatist militias. Many nonpartisan sources believe that officials within Pakistan's military and the ISI sympathise with and aid Islamic terrorists, saying that the "ISI has provided covert but well documented support to terrorist groups active in Kashmir, including the al Qaeda affiliate Jaish e Mohammed". General Javed Nasir confessed to assisting the besieged Bosnian Muslims, supporting Chinese Muslims in Xinjiang despite a UN arms embargo, rebel Muslim groups in the Philippines, and some religious groups in Central Asia. The National Intelligence Coordination Committee (NICC) of Pakistan is headed by the Director General of Inter Services Intelligence. The overarching intelligence coordination body was given assent by the Prime Minister of Pakistan in November 2020. It held its inaugural session on 24 June 2021, marking the date the committee became functional.

Covert Action Division: Its roles are similar to the Special Activities Division of the CIA and a handful of officers are trained by that division. The division has been active since the 1960s. Joint Intelligence X: Coordinates the other departments in the ISI. The department has been inactive since March 2012 with the new director general taking operational charge of the ISI.

The army has ruled Pakistan for more than half of its history and has always been unwilling to see its influence being compromised by any civilian leaders. In the 1990s, Prime Minister Benazir Bhutto appointed retired army officer Shamsur Rahman Kallu as director general, but army leaders refused to cooperate with Kallu because he had refused to engage in martial law duties under the previous dictator. In October 1998, Ziauddin Butt was chosen as director general. Though Butt was not the preferred choice of Prime Minister Nawaz Sharif, he grew close with him, and Chairman Joint Chiefs of Staff Committee General Pervez Musharraf took over important ISI files. During a military coup a year later, Musharraf arrested Butt, who had been promoted to Chief of Army Staff by Sharif. On 6 October 2016, the daily newspaper Dawn published a report about a government meeting allegedly arranged by Sharif. The article detailed a presentation by Foreign Secretary Aizaz Chaudhry about international pressure to crack down on Pakistan's extremist segments such as Masood Azhar, the Jaish i Mohmmad, Hafiz Saeed, the Lashkar e Taiba, and the Haqqani network. According to Ghazi Salahuddin of The News International, controversy ensued after the October meeting and the Dawn report, which lingered until May 2016. During the October 2016 meeting, Punjab chief minister Shahbaz Sharif allegedly revealed that, whenever action had been taken against certain extremist groups by civilian authorities, the security agency had worked secretly to free the arrested parties. On 6 October 2021, the Pakistan military's media affairs wing announced the replacement of Faiz Hameed with Nadeem Anjum. After two days, it became apparent on social media that the federal government of Pakistan had yet to issue any formal notification for the appointment of the new director general. Rumors became more substantiated when Hameed attended the National Security Committee meeting instead of the expected new director general. Walsh said that the complex "resembles a well funded private university" and that the buildings are "neatly tended," the lawns are "smooth," and the fountains are "tinkling." He described the central building, which houses the director general's office on the top floor, as "a modern structure with a round, echoing lobby".

1982–1997: ISI is believed to have had access to Osama bin Laden in the past. B. Raman, former Research and Analysis Wing (R&AW) officer, claims that the Central Intelligence Agency through the ISI promoted the smuggling of heroin into Afghanistan to turn Soviet troops into heroin addicts and thus greatly reduce their fighting potential. 1986: Worrying that among the large influx of Afghan refugees who had come into Pakistan because of the Soviet–Afghan War were members of KHAD (Afghan Intelligence), the ISI convinced Mansoor Ahmed, who was the chargé d'affaires of the Afghan embassy in Islamabad, to turn his back on the Soviet backed Afghan government. He and his family were secretly escorted out of their residence and given safe passage on a London bound British Airways flight in exchange for classified information in regard to Afghan agents in Pakistan. The Soviet and Afghan diplomats did not find his family. 1990: According to Peter Tomsen, the United States Special Envoy to Afghanistan, neighboring Pakistan had tried to bring Gulbuddin Hekmatyar to power in Afghanistan against the opposition of all other mujahideen commanders and factions as early as 1990. In October 1990, the ISI had devised a plan for Hekmatyar to conduct a mass bombardment of the Afghan capital Kabul, then still under communist rule, with possible Pakistani troop reinforcements. According to Pakistani Afghanistan expert Ahmed Rashid, "between 1994 and 1999, an estimated 80,000 to 100,000 Pakistanis trained and fought in Afghanistan" on the side of the Taliban. 2008: Militants attacked the Indian Consulate General in Jalalabad in 2007. According to Afghanistan's National Directorate of Security, individuals arrested by the Afghan government stated that the ISI was behind the attack and had given them ₹120,000 for the operation. 2001 onwards: American officials believe members of the Pakistani intelligence service are alerting militants to imminent American missile strikes in Pakistan's tribal areas. In October 2009, Davood Moradian, a senior policy adviser to foreign minister Rangeen Dadfar Spanta, said the British and American governments were fully aware of the ISI's role but lacked the courage to confront Islamabad. He claimed that the Afghan government had given British and American intelligence agents evidence that proved ISI involvement in bombings. 2010: A new report by the London School of Economics (LSE) claimed to provide the most concrete evidence that the ISI is providing funding, training, and sanctuary to the Taliban insurgency on a scale much larger than previously thought. The report's author, Matt Waldman, spoke to nine Taliban field commanders in Afghanistan and concluded that Pakistan's relationship with the insurgents ran far deeper than previously realised. Some of those interviewed suggested that the organisation even attended meetings of the Taliban's supreme council, the Quetta Shura. A spokesman for the Pakistani military dismissed the report, describing it as "malicious". General David Petraeus, commander of the US Central Command, refused to endorse this report in a US congressional hearing and suggested that any contacts between ISI and extremists are for legitimate intelligence purposes; in his words, "you have to have contact with bad guys to get intelligence on bad guys". 2021: The Fall of Kabul was seen as a major strategic victory for ISI that has long been seeking a pro Pakistan government in Kabul. ISI has always aspired to see Islamists as a rulers of Taliban. The rise of Taliban in Kabul was considered as an achievement for ISI's strategic depth in Afghanistan. 2021: It was reported that ISI mediated talks between different factions of Taliban on the power sharing. ISI ensured Haqqani Network holds lion's share in the Taliban's Cabinet of Afghanistan.

1993: The ISI was involved in supplying arms to the Bosnian mujahideen in Bosnia Herzegovina to prevent a total genocide of Muslims at the hands of the Serbs.

Indian intelligence agencies have claimed they have proof of ISI involvement with the Naxalites. ISI is also reportedly engaged in supporting Khalistani Separatism in India. A classified report accessed by the Indian newspaper Asian Age said "the ISI in particular wants Naxals to cause large scale damage to infrastructure projects and industrial units operating in the interior parts of the country where ISI's own terror network is non existent". 1965: The Indo Pakistani War of 1965 in Kashmir provoked a major crisis in intelligence. When the war began, there was a complete collapse of operations across all intelligence agencies. They were unable to locate an Indian armored division because of their preoccupation with political affairs. Ayub Khan set up a committee headed by General Yahya Khan to examine the agencies' workings. 1969–1974: According to Indian spymaster B. Raman, the Central Intelligence Agency and ISI worke with the Nixon administration to assist the Khalistan movement in Punjab. 1980: An Indian agent captured by the PAF Field Intelligence Unit in Karachi said the leader of the spy ring was being headed by the food and beverages manager at the Intercontinental Hotel in Karachi and a number of serving Air Force officers and ratings were on his payroll. The ISI decided to question the manager to see who he was in contact with, but the former president of Pakistan, Zia ul Haq, intervened and wanted the manager and anyone else involved in the case arrested immediately. The manager was proven completely innocent afterwards. India mountedOperation Meghdoot and captured the entire glacier. 1988: The ISI implemented Operation Tupac, a three part action plan for covertly supporting Kashmiri militants in their fight against Indian authorities in Kashmir, initiated by President Zia ul Haq in 1988 After the success of Operation Tupac, support of Kashmiri militants became Pakistan's state policy. ISI is widely believed to train and support militancy in the Kashmir region. 2014: In February (disclosed in March 2015), the then Indian chief of army staff General Bikram Singh issued orders to deploy troops along the borders with Pakistan in the Rajasthan and Jammu Kashmir regions, but the ISI got the information in a few hours and in reaction the Pakistan Army deployed its troops near the Indian borders, which alarmed Indian authorities. 2016: Home Minister Balochistan, Pakistan, Sarfraz Bugti stated on 26 March that a serving Indian Naval officer, Kulbhushan Yadav, was arrested in Balochistan by the ISI.

The ISI was accused of being involved in the Mehran bank scandal, in which high ranking ISI and Army officers were allegedly given large sums of money by Yunus Habib, owner of the Mehran Bank, to deposit the ISI's foreign exchange reserves in his bank. 1980: The ISI became aware of a plot to assassinate Zia ul Haq and launch a coup to depose replace the government with an Islamic one. The attempted assassination and coup were planned for 23 March 1980, during the annual 23 March Pakistan Day Parade. The masterminds behind the coup were high ranking military and intelligence officers, and were led by Major General Tajammal Hussain Malik; his son Captain Naveed; and his nephew Major Riaz, a former military intelligence officer. The ISI decided against arresting the men outright because they did not know how deep the conspiracy went, and kept them under strict surveillance. As the date of the annual parade approached, the ISI was satisfied that it had identified the major players in the conspiracy and arrested the men along with some high ranking military officers. 1990: The 1990 elections were widely believed to have been rigged by the ISI in favor of the Islami Jamhoori Ittehad (IJI) party, a conglomerate of nine mainly rightist parties by the ISI under Lieutenant General Hameed Gul, to ensure the defeat of Bhutto's Pakistan Peoples Party (PPP) in the polls. 2000s: The ISI engaged with Pakistan armed forces in the War in North West Pakistan against Tehrik i Taliban Pakistan, and is reported to have lost 78 ISI personnel. 2006: Rangzieb Ahmed brought a civil claim against MI5 for suggesting the ISI arrested him in 2006 and colluded in torturing him by submitting questions which were put to him under torture in Pakistan. 2011: The ISI arrested five Pakistanis who worked as CIA informants who passed information that led to the death of Osama bin Laden. However, among them in particular, the US was trying to seek the release of Shakil Afridi, who ran a fake vaccination campaign that provided critical intelligence for the raid on the bin Laden compound. However, the Pakistani government and military establishment refused to release Afridi, who has since been serving a 33 year prison sentence.

1979: The ISI discovered a surveillance mission at the Kahuta Research Laboratories nuclear complex on 26 June 1979 by the French Ambassador to Pakistan Le Gourrierec and First Secretary Jean Forlot. Both were arrested and their cameras and other sensitive equipment were confiscated. Documents intercepted later showed that the two were recruited by the CIA.

1980s: The ISI intercepted two American private sector weapons dealers during the Soviet Afghan war of the 1980s. One American diplomat lived in the F 7/4 sector of Islamabad and was spotted by an ISI agent in a seedy part of Rawalpindi, drawing attention because of his automobile's diplomatic plates. He was bugged and subsequently trailed and found to be in contact with tribal groups and supplying them with weapons for their fight against the Soviet Army in Afghanistan. The second American weapons dealer was Eugene Clegg, a teacher in the American International School. One American International School employee and undercover agent, Naeem, was arrested while waiting to clear a shipment from Islamabad customs. All of them were put out of business. Former director general Ashfaq Parvez Kayani is also reported to have said, the "real aim of U. S. [war] strategy is to denuclearize Pakistan". 2011: In the aftermath of a shooting involving American CIA agent Raymond Davis, the ISI became more alert and suspicious about the CIA's spy network in Pakistan, which had disrupted ISI CIA cooperation. At least 30 suspected covert American operatives have suspended their activities in Pakistan and 12 have reportedly left the country. A Chinese woman believed to be an ISI agent, who headed the Chinese unit of a US manufacturer, was charged with illegally exporting high performance coatings for Pakistan's nuclear power plants. Xun Wang, a former managing director of PPG Paints Trading in Shanghai, a Chinese subsidiary of United States based PPG Industries, Inc., was indicted on a charge of conspiring to violate the International Emergency Economic Powers Act and related offences. Wang was accused of conspiring to export and re export specially designed, high performance epoxy coatings to the Chashma 2 Nuclear Power Plant in Pakistan via a third party distributor in the People's Republic of China. Alleged ISI operative Mohammed Tasleem, an attaché in the New York consulate, was discovered to be issuing threats against Pakistanis living in the United States to prevent them from speaking openly about Pakistan's government in 2010 by the FBI. US officials and scholars say the ISI has a systematic campaign to threaten those who speak critically of the Pakistani military.

2000s: ISI played pivotal role in crushing Tamil Insurgency in Sri Lanka which was being supported by India's RAW to carve out separate Tamil country for the Tamils of Sri Lanka. ISI, in response to the RAW's machinations, started to equip, train and provide logistical support to the Sri Lankan Armed Forces in their war against Tamil rebels. ISI supplied multi barrel rocket launcher systems and other weaponry, which halted the offensive. ISI, by supplying high tech military equipment such as 22 Al Khalid main battle tanks, 250,000 rounds of mortar ammunition and 150,000 hand grenades, and sending army officers to Sri Lanka, played a key role in the ultimate defeat of Tamil Tigers in May 2009. The victory of Sri Lankan Armed Forces on Tamil Tigers ultimately strengthened Pakistan Sri Lanka ties. 2011: ISI started to train State Police of Sri Lanka and Sri Lankan State Intelligence Service on intelligence gathering.

Ramzi Yousef: One of the planners of the 1993 World Trade Center bombing and the Bojinka plot. Pakistani intelligence, and the Department of State – U. S. Diplomatic Security Service (DSS) Special Agents, captured Yousef in Islamabad, Pakistan. On 7 February 1995, they raided room number 16 in the Su Casa Guest House in Islamabad and captured Yousef before he could move to Peshawar. Ibn al Shaykh al Libi: A Libyan paramilitary trainer for Al Qaeda, attempted to flee Afghanistan in November 2001 following the collapse of the Taliban, precipitating the 2001 U. S. invasion of Afghanistan. He was captured by Pakistani forces. Ahmed Omar Saeed Sheikh: A British born terrorist of Pakistani descent who was arrested by Pakistani police on 12 February 2002 in Lahore for his involvement with the Pearl kidnapping. Pearl had been kidnapped, had his throat slit, and then beheaded. He was named the chief suspect, but claimed he had surrendered to the ISI a week earlier. Abu Zubaydah: An Al Qaeda terrorist responsible for conceiving multiple terrorist plots, including sending Ahmed Ressam to blow up the Los Angeles airport in 2000. He was captured on 28 March 2002, by ISI, CIA, and FBI agents after they raided several safe houses in Faisalabad, Pakistan. Ramzi bin al Shibh: An Al Qaeda terrorist responsible for planning the 9/11 terrorist attacks, the USS Cole bombing, and the 2002 Ghriba synagogue bombing in Tunisia. On 11 September 2002, the ISI captured Ramzi bin al Shibh during a raid in Karachi. Khalid Sheikh Mohammed: The principal architect of the 9/11 attacks and other significant terrorist plots over the last twenty years, including the World Trade Center 1993 bombings, the Bojinka plot, an aborted 2002 attack on the U. S. Bank Tower in Los Angeles, the Bali nightclub bombings, the failed bombing of American Airlines Flight 63, the Millennium Plot, and the murder of Daniel Pearl. On 1 March 2003, the ISI captured him in a joint raid with the CIA's Special Activities Division paramilitary operatives and Diplomatic Security Service Special Agents in Rawalpindi, Pakistan. Abu Faraj Farj al Liby: Mastermind of two failed attempts on President Pervez Musharraf's life in May 2005. Maulvi Omar: Senior aid to Baitullah Mehsud, who was captured by the ISI in August 2009. Abdul Ghani Baradar: The Taliban's deputy commander who was captured by Pakistani intelligence forces in or near Karachi, Pakistan, in early 2010.

Critics of the ISI say that it has become a state within a state and not accountable enough. Some analysts say that it is because intelligence agencies around the world remain secretive. Critics argue the institution should be more accountable to the president or the prime minister. The Pakistani government disbanded the ISI's political wing in 2008 after its discovery.

During the Cold War, the ISI and the CIA worked together to send spy planes over the Soviet Union. The two organisations also worked closely during the Soviet–Afghan War supporting groups such as Gulbuddin Hekmatyar's Hezb i Islami and Jalaluddin Haqqani, leader of the Haqqani network. Some report the ISI and CIA stepped up cooperation in the aftermath of the 9/11 attacks to kill and capture senior Al Qaeda leaders such as Sheikh Younis Al Mauritan and Khalid Shaikh Mohammed, the planner of the 9/11 attacks who was residing in Pakistan. Pakistan claims that around 100 top level al Qaeda leaders/operators were killed or arrested by the ISI. Secretary of State Hillary Clinton said Pakistan is paying a "big price for supporting the U. S. war against terror groups. [ ] I think it is important to note that as they have made these adjustments in their own assessment of their national interests, they're paying a big price for it." Other senior international officials maintain that senior Al Qaeda leaders such as bin Laden have been hidden by the ISI in major settled areas of Pakistan with the full knowledge of the Pakistani military leadership. A December 2011 analysis report by the Jamestown Foundation came 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 former Chief of Army Staff (COAS) General Ashfaq Pervez Kayani. Former Pakistani General Ziauddin Butt (a. k. a. General Ziauddin Khawaja) revealed at a conference on Pakistani U. S. relations in October 2011 that according to his knowledge the then former Director General of Intelligence Bureau of Pakistan (2004–2008), Brigadier Ijaz Shah (retd. ), had kept Osama bin Laden in an Intelligence Bureau safe house in Abbottabad. Pakistani general Ziauddin Butt said bin Laden had been hidden in Abbottabad by the ISI "with the full knowledge" of General Pervez Musharraf U. S. military officials have increasingly said they do not notify Pakistani officials before conducting operations against the Afghan Taliban or Al Qaeda, because they fear Pakistani officials may tip them off. International officials have accused the ISI of continuing to support and even lead the Taliban during the 2001 2021 War in Afghanistan. As Chairman of the Joint Chiefs of Staff, Mike Mullen stated:

The fact remains that the Quetta Shura [Taliban] and the Haqqani Network operate from Pakistan with impunity Extremist organizations serving as proxies of the government of Pakistan are attacking Afghan troops and civilians as well as US soldiers. For example, we believe the Haqqani Network—which has long enjoyed the support and protection of the Pakistani government is, in many ways, a strategic arm of Pakistan's Inter Services Intelligence Agency. The Associated Press reported that "the president said Mullen's statement 'expressed frustration' over the insurgent safe havens in Pakistan. But Obama said 'the intelligence is not as clear as we might like in terms of what exactly that relationship is.' Obama added that whether Pakistan's ties with the Haqqani network are active or passive, Pakistan has to deal with it." The Guantanamo Bay files leak showed that the US authorities unofficially consider the ISI a terrorist organization that was equally as dangerous as Al Qaeda and the Taliban, and many allegations of it supporting terrorist activities have been made. In 2017, General Joseph Dunford, chairman of the Joint Chiefs of Staff, accused the ISI of having ties to terror groups. In a Senate hearing, Dunford told members of the U. S. Senate: "It is clear to me that the ISI has connections with terrorist groups."

India has accused the ISI of plotting the 1993 Bombay bombings. According to the United States diplomatic cables leak, the ISI had previously shared intelligence information with Israel regarding possible terrorist attacks against Jewish and Israeli sites in India in late 2008. The ISI is also accused of supporting pro independence militias in Jammu and Kashmir while Pakistan denies all such claims, or says it gives them moral support only. According to Grant Holt and David H. Gray, "The agency specializes in utilizing terrorist organizations as proxies for Pakistani foreign policy, covert action abroad, and controlling domestic politics." James Forest says, "There has been increasing proof from counter terrorism organizations that militants and the Taliban continue to receive assistance from the ISI, as well as the establishment of camps to train terrorists on Pakistani territory." All external operations are carried out under the supervision of the ISI's S Wing. Joint Intelligence/North is responsible for conducting operations in Jammu and Kashmir and Afghanistan. The Joint Signal Intelligence Bureau (JSIB) provides support with communications to groups in Jammu and Kashmir.

Since the 1990s, the ISI began communicating with the jihadists who emerged from the conflict against the Soviet Union in Afghanistan, and by 2000 most militant groups operating in Kashmir were based in Pakistan or were pro Pakistan. These groups are used to conduct a low intensity conflict against India. According to Stephen P. Cohen and John Wilson, the ISI's aid to and creation of designated terrorist groups and religious extremist groups is well documented. The ISI has been accused of having close ties to Lashkar e Taiba, who carried out the attacks in Mumbai in 2008. The organisation has also given aid to Hizbul Mujahideen. Terrorism expert Gus Martin said, "The ISI has a long history of supporting designated terrorist groups and pro Independence groups operating in Punjab and Jammu and Kashmir which fight against Indian interests." The ISI also helped with the founding of the group Jaish e Mohammed.

The group Hizbul Mujahideen was created as the Kashmiri branch of Jamaat i Islami. It was reported that JI founded Hizbul Mujahideen at the request of the ISI to counter the Jammu and Kashmir Liberation Front who are advocates for the independence of Kashmir. The failure of 1987 elections in Kashmir, and afterwards the arrest of Muhammad Yusuf, a. k. a. Syed Salahuddin, led to the events that created armed struggle in the valley.

There have been three incarnations of Al Badr. According to Tomsen, the ISI, in conjunction with Jamaat e Islami, formed the first Al Badr, who resisted the Indian trained influx of Mukti Bahini in Bangladesh in the 1970s.

The ISI supported Al Qaeda during the war along with the CIA against the Soviet government, through the Taliban, and it is believed by some that there is still contact between Al Qaeda and the ISI. An assessment by British Intelligence in 2000 into Al Qaeda training camps in Afghanistan showed the ISI were playing an active role in some of them. In 2002, it was alleged that when the Egyptian investigators tracked down Al Qaeda member Ahmed Said Khadr in Pakistan, the Egyptian authorities informed Pakistani authorities of his location. However, the Afghan Taliban at night came in a car and took Khadir along with them to Afghanistan. The next day, Pakistani authorities claimed they were unable to capture Khadir. The leak in 2012 of e mails from Stratfor claimed papers captured during all the compounds during the raid in Abbottabad on Osama bin Laden's compound showed up to 12 ISI officials knew where he was and that Bin Laden had been in regular contact with the ISI. Despite the allegations, Steve Coll stated that as of 2019 there is no direct evidence showing Pakistani knowledge of bin Laden's presence in Abbottabad, even by a rogue or compartmented faction within the government, other than the circumstantial fact of bin Laden's compound being located near (albeit not directly visible from) the Pakistan Military Academy. Documents captured from the Abbottabad compound generally show that bin Laden was wary of contact with ISI and Pakistani police, especially in light of Pakistan's role in the arrest of Khalid Sheikh Mohammed; it has also been suggested that the $25 million U. S. reward for information leading to bin Laden would have been enticing to Pakistani officers given their reputation for corruption. The compound itself, although unusually tall, was less conspicuous than sometimes envisaged by Americans, given the common local habit of walling off homes for protection against violence or to ensure the privacy of female family members. Al Qaeda has repeatedly labelled ISI their enemy, and claimed the Pakistani military and intelligence are their main targets in Pakistan. In 2019, Ayman al Zawahari labelled ISI and the Pakistani military a "puppet" of the United States in a video message.

The Harkat ul Mujahideen was founded in the 1980s by the ISI to fight against Indian interests.

in 1984, under the orders of Zia ul Haq, the ISI prepared for a rebellion, which was to be set in motion in 1991.

The ISI allegedly have links to the Haqqani network and contributed to their funding. It is widely believed the suicide attack on the Indian embassy in Kabul in 2008 was planned with the help of the ISI. A report in 2008 from the US director of National Intelligence stated that the ISI provides intelligence and funding to help with attacks against the International Security Assistance Force, the Afghan government, and Indian targets. On 5 November 2014, Lieutenant General Joseph Anderson, a senior commander for US and NATO forces in Afghanistan, said that the Haqqani network is now "fractured" like the Taliban in a Pentagon hosted video briefing from Afghanistan. "They are fractured. They are fractured like the Taliban is. That's based pretty much on Pakistan's operations in North Waziristan this entire summer fall," he said, acknowledging the effectiveness of Pakistan's military offensive in North Waziristan. "That has very much disrupted their efforts in Afghanistan and has caused them to be less effective in terms of their ability to pull off an attack in Kabul," Anderson added.

Amnesty International published a document concerning the investigation of ISI over the murder of Saleem Shahzad.

Since Pakistan launched offensives on Al Qaeda, the Taliban, and other jihadist groups, the country's armed forces, intelligence services (particularly the ISI), military industrial complexes, paramilitary forces, and police forces have come under intense attacks. The ISI has played a major role in targeting these groups and has faced retaliatory strikes as well. as of 2011, more than 300 ISI officials have been killed. Major incidents when attempts were made to target the ISI include:
A suicide bomber drove his vehicle into a bus carrying officials killing at least 28 people on 28 November 2007, outside the ISI office in Rawalpindi. 30 people, including four ISI officials and 14 policemen, were killed and over 300 were injured when three people attacked the ISI office in Lahore on 27 May 2009. The attackers fired at the ISI office and policemen present there. The guards at the ISI building fought back. During the incident an explosive laden vehicle detonated. At least 13 people and 10 military personnel were killed when a suicide bomber blew up his van at the agency's Peshawar office on 13 November 2009. Around of explosives were used which destroyed a significant portion of the building. Two attackers ambushed the Multan office where eight people were killed and 45 were injured on 8 December 2009. Two army personnel were killed while seven officials were injured. About of explosives were used. A car bomb exploded at CNG Station in Faisalabad on 8 March 2011, killing 25 people and injuring more than 100. Taliban spokesman Ehsanullah Ehsan said that the nearby ISI office was the target. No losses of ISI personnel were reported, and only one official was injured. Three intelligence officials were killed and one was wounded when a vehicle carrying agency personnel was ambushed in FR Bannu on 14 September 2011. Four people, including ISI officials, were killed and 35 were injured when the local office of the ISI was attacked by five suicide bombers in Sukkur on 24 July 2013.