On the eve of the launch of the war against the Iranian regime by Israel and the United States – which is spreading throughout the region – Pakistan and Afghanistan exchanged missile fire.Shortly after the first strikes of Operation Epic Fury, US President Donald Trump called on Iranian minorities to rise up against the regime – notably the Baloch, a people also present in Pakistan and Afghanistan and driven by strong irredentism.In Iran, the spearhead of this Baloch irredentist is Jaysh al-Adl, a Sunni group with jihadist leanings that since the early 2010s has been stepping up attacks against the Iranian authorities, using Pakistan and Afghanistan as rear bases. While Tehran has long accused Islamabad of not cracking down hard enough on these terrorists, in 2024 Iran bombed some of their training camps in Pakistan. In response, Pakistan attacked certain Baloch positions in Iran in a large-scale operation.These operations reflect the concern that Baloch separatism is causing in Islamabad and Rawalpindi, where the Pakistani army headquarters is located. For more than 20 years, the Balochistan Liberation Army (BLA), despite fierce repression, has acquired a great striking power. In January 2026, it was behind a series of attacks in Pakistan, targeting police stations, military personnel, and prisons. Following these attacks, Pakistan accused foreign powers of supporting the BLP. While Afghanistan and Iran were the primary targets, Islamabad also claimed that India had infiltrated secret agents into Pakistan with the aim of encouraging separatism.These various episodes reveal a game of influence: India is seeking to use Iran to put Pakistan in a pincer movement, as it is trying to do with Afghanistan. Recent developments thus show that the Central Asian (Afghan-Pakistani), South Asian (Indo-Pakistani), and Middle Eastern theaters, while retaining a regional logic, can interact with each other. In this new configuration, two coalitions are emerging. One includes the United States, Israel, the United Arab Emirates, India, and even Afghanistan. The other includes Saudi Arabia, Pakistan, Turkey, and China.This perspective, like the ongoing conflicts in other parts of the world, requires observers to combine a detailed knowledge of the societies in question with an analysis of their foreign and defense policies. The new situation at the crossroads Middle of the East (Iran), Central Asia (Afghanistan), and South Asia (Pakistan and India) could thus result from both Baloch separatism and India’s strategy in the region.Pakistan-Afghanistan: The historical roots of a warToday’s open conflict between Pakistan and Afghanistan is of unprecedented intensity: never before have the two countries been at war with each other in this way.Local residents stand next to a damaged car at the site of a cross-border Pakistani army strike in the Behsud district of Nangarhar province in Afghanistan on February 22, 2026. Photo: AP/PTI.However, the roots of this antagonism are long-standing, for at least three reasons.First, the issue of borders remains a bone of contention for both the countries. This is crystallised around the fate of the Pashtun ethnic group, which each side seeks to incorporate within its own borders.Second, Kabul and Islamabad’s views on Islamism are increasingly incompatible. To counter Afghan-Pashtun ethno-nationalism, Pakistan supported the early Afghan Islamists, whom it then armed during the first war in Afghanistan. After the defeat of the Soviet Union, it also helped the Taliban seize power.After September 11, Pakistan played a double game due to American pressure, which alienated some of the most radical groups. Even though Pakistan continued to rely on the Taliban, their return to power after the US withdrawal from Afghanistan did not lead them to bring the organisations that had become hostile to Islamabad into line. This antagonism can be explained in part by the Taliban’s desire – already apparent in the years 1996-2001 – to free themselves from the tutelage of their neighbour.Third, Pakistan fears being caught in a pincer movement between Afghanistan and India. This fear remains a factor in Islamabad’s attitude towards Kabul and largely explains the strikes in Afghanistan in recent months. These strikes may have surprised observers who had not been following regional developments closely: Islamabad had in fact welcomed the withdrawal of US troops ordered by Biden in 2021 and the subsequent return of the Taliban.These three reasons for conflict are only independent in appearance: in reality, they are interrelated. In seeking to curb Pashtun irredentism since the country’s creation, Pakistan has helped to strengthen those who would become its enemies.Drawing borders: the importance of Pashtun nationalismOne of the most significant disagreements between Afghans and Pakistanis concerns ethnic and territorial issues. While Kabul believes that all Pashtuns should live within the country’s borders, Islamabad considers those east of the Durand Line to be subjects of the Pakistani state.This structural divergence of opinion is as old as Pakistan itself.In 1947, Pashtun leaders of the North West Frontier Province, a province of the British Raj that they dominated, were not in favour of the Partition but supported the views of Mahatma Gandhi, who opposed the division of the country. While their resistance was quickly crushed by force, the hostility of the Afghans was much more problematic. In June 1947, Afghan Prime Minister Mohammad Hashim Khan had declared: “If an independent Pashtunistan cannot be established, then [the North West Frontier Province] should join Afghanistan.”This did not happen. When India was partitioned in August 1947, Afghanistan was the only country to vote against Pakistan’s admission to the United Nations, for reasons put forward by the Afghan representative: the country could not “recognise the North West Frontier Province as part of Pakistan until [its population] has had the opportunity, without any influence, to determine for itself whether it wishes to be independent or part of Pakistan.”Pakistan’s opposition to this redrawing of borders was partly motivated by a fear of encirclement.As General Ayub Khan, the country’s strongman from 1958 to 1969, confided, Pakistani leaders were convinced that Kabul and New Delhi were trying to encircle their country. In 1949, when Afghanistan officially rejected the Durand Line, “Pachtounistan Day,” which Kabul had set for August 31, was celebrated in many Indian cities.After a period of decline or stagnation, Pashtun nationalism returned with a vengeance in Afghanistan in the 1970s, when it was once again supported by propaganda emanating from Kabul under the aegis of Mohammad Daoud Khan, president of the country from 1973 to 1978.Daoud, who had promoted this political line when he was prime minister between 1953 and 1963, had been marginalised by King Zahir Shah. Returning in 1973, he deposed the king and became president of Afghanistan. During his early years as head of state, he said he wanted to work towards the creation of an independent Pashtunistan based on the model of Bangladesh, which was founded in 1971, in cooperation with Ajmal Khattak, the secretary-general of the Pakistani Pashtun nationalists in exile in Kabul. Relations with Islamabad were further weakened when Afghanistan published maps incorporating the Pashtun region of Pakistan within the country’s borders.Curbing irredentism: Pakistan’s Islamist cardIt was largely in response to this Afghan and Pashtun ethno-nationalist threat that Zulfikar Ali Bhutto brought Pakistan’s support to young Afghan Islamists who were mobilising against Daoud – whom they perceived as the gravedigger of their faith and a vassal of the Soviet Union, which was then seeking to expand southward.Bhutto believed that these forces were likely to destabilise the government in Kabul. Among the Islamists were three names that would become leaders of the anti-Soviet jihad: Burhanuddin Rabbani, Gulbuddin Hekmatyar, and Ahmed Shah Massoud, all students at Kabul University. All three were “selected for commando training at Cherat,” the military base where Pakistani special forces trained, 50 kilometers southeast of Peshawar.The Soviet invasion of Afghanistan gave Pakistan the opportunity to advance on two fronts.On the one hand, the country could hope to neutralise Afghan-Pashtun nationalism in the name of defending religion. In addition to the Afghan mujahideen, the Pakistanis equipped and trained Islamists from all over the world during the war in Afghanistan. This policy, which led to the recruitment of Arab, Uzbek, North African, and other militants, was implemented from 1983 onwards with the help of Saudi Arabia – with Prince Turki, the Saudi minister of intelligence, playing a key role – and the United States.On the other hand, by supporting a government that it would help bring to power in Kabul, Pakistan hoped to gain “strategic depth” vis-à-vis India by turning Afghanistan into a protectorate.From 1994 onwards, this calculation guided Islamabad’s support for the Taliban, who, after the Soviet withdrawal and several years of civil war, appeared to be the most serious contenders for power. In the fall of that same year, Benazir Bhutto’s government sided with them.Less than two years later, the Taliban took Kabul with the help of Pakistan’s Inter-Services Intelligence (ISI). Pakistan was the only country, along with Saudi Arabia and the United Arab Emirates, to recognise their government.Pakistan put to the test by international jihadContrary to the hopes of the Pakistani people, however, the Taliban government resisted Islamabad’s influence in the name of national sovereignty. This resistance by the Taliban to Pakistani pressure was particularly strong on the territorial front: they refused to recognise the Durand Line as an international border.In his autobiography, Abdul Salam Zaeff, Taliban ambassador to Islamabad in 2000-2001, shows how tense the relations between Afghanistan and Pakistan were due to conflicts between national sovereignties and nationalisms. Considering this relationship from a historical perspective, he writes: “The wolf and the sheep may drink from the same stream, but since the beginning of the jihad, the ISI has spread its roots in Afghanistan, like cancer taking root in the human body; all Afghan leaders have complained about it, but none have been able to get rid of it.”This situation presented Pakistan with a real dilemma at the turn of the 21st century. The protection that Pakistan offered the Taliban damaged its image in the West. Islamabad found itself at odds with Afghan nationalism among the Taliban due to its support for international jihad, which had taken root in the country since the Afghan war. The presence of Bin Laden, who settled there in 1996 with ISI support, exemplified this. The US deemed this support reprehensible as early as 1998, following Al Qaeda’s attacks on American embassies in Nairobi and Dar es Salaam.The attacks of September 11, 2001, forced Pakistan to choose. While the Taliban continued to protect Al-Qaeda, the Bush administration demanded that Pakistan assist the United States in conducting operations in Afghanistan to dismantle bin Laden’s networks and end the regime in Kabul.As the head of Pakistan since the 1999 coup, general Pervez Musharraf sought to maintain strong relations with the Taliban, but was forced to make concessions to the US, he handed over Al-Qaeda leaders to Washington and targeted certain Islamist groups.In 2007, this policy led him to storm the Red Mosque in Islamabad, which was an integral part of this network. This operation led Islamist groups in the tribal areas of the Pashtun region, or “FATA,” , enclaved in the North-West Frontier Province, to mobilise by creating the Tehrik-i-Taliban Pakistan (TTP).When it was formed, the TTP pledged allegiance to Mullah Mohammad Omar, who continued to lead the Taliban from Kandahar. From Pakistani territory, it carried out guerrilla operations against US troops, which numbered 130,000 as of 2009.Faced with this irregular war, the United States obtained information from the Pakistanis necessary to conduct drone strikes. In response, the TTP stepped up its attacks on Pakistani soil, even targeting the capital.The Pakistani army responded with fierce repression, which reached its peak in the FATA in 2013-2015: Pakistani generals had come to fight against some of the groups they had armed and trained in the 1980s and 1990s.While making concessions to the United States, Islamabad continued to support the Afghan Taliban, whom it hoped would return to power. This was all the more desirable given that, thanks to Washington’s intervention and the installation of Hamid Karzai and then Ashraf Ghani as leaders of Afghanistan, India was gaining important positions in the country. New Delhi was opening consulates, building roads, financing hospitals, and working to connect India to Afghanistan via Iran–Tehran having ceded part of the port of Chabahar to India.Pakistan feared only one thing: being surrounded by its three neighbours. This fear explained the resurgence of terrorist attacks in India from 2016 onwards , following Narendra Modi’s decision to deliver combat helicopters to Afghanistan.The “betrayal” of the TalibanWhen the Taliban returned to power in 2021 after the withdrawal of the United States, Pakistan once again tried to exert its influence over Afghanistan. However, it encountered even greater resistance than in the years 1996-2001.The new Taliban government proved even more protective of its national sovereignty than its predecessor: it too refuses to recognise the Durand Line as an international border. This refusal led the Pakistanis to materialise the border by imposing a veritable barrier on Afghanistan, the construction of which – begun in 2013, notably to control drug trafficking – was completed in 2022. To make it clear that, from now on, “everyone in their own country” was the rule, Islamabad also sent back to “their” country more than a million Afghan refugees who had sought asylum in Pakistan, some of them more than 40 years ago.This human and humanitarian catastrophe was also a form of retaliation. The Taliban government had chosen to protect the TTP, which had already found refuge in areas gradually abandoned by US troops in eastern Afghanistan, from where it was attacking Pakistan. These attacks intensified after the Taliban released many TTP prisoners who had been captured by US and Afghan troops under Karzai and Ghani. Afghanistan thus became the base from which the TTP strikes Pakistan with renewed vigour. Attacks have multiplied, not only in the Pashtun area, but also in Islamabad.As a result of this, the Pakistani army launched a major military operation targeting TTP leader Noor Wali Mehsud on October 9, 2025. In retaliation, the Afghan army attacked Pakistani army posts on the border. The Pakistani army responded by targeting not only TTP training camps, but also Afghan Taliban positions in Kandahar and Helmand provinces.To prevent an escalation and negotiate a truce, Qatar and Turkey intervened to open talks and, during the truce that was thus achieved, Kabul announced that it was ending its support for the TTP.However, the détente was short-lived. On February 6, an attack in Islamabad targeting a Shia mosque left 32 dead and 160 wounded: it was claimed by a branch of the Islamic State (IS), IS-K, created in 2015 from a group of fighters recruited by the TTP to fight in Syria from 2012 alongside Abu Bakr al-Baghdadi’s troops.IS-K received assistance from the Haqqani network, a component of the Pakistani Taliban movement. From 2016 onwards, it carried out terrorist operations targeting mainly Pakistan and certain minorities such as the Hazaras (Shiites). Although the Kabul government officially sought to crack down on it from 2022 onwards, its leader Sanaullah Ghafari nevertheless maintained his headquarters in Kabul.While IS-K bases were located in the provinces of Kunar and Logar in Afghanistan, the Pakistani army responded to the February 6 attack with large-scale airstrikes targeting TTP and IS-K training camps. The toll, according to Islamabad , was 80 dead.On February 26, the Afghan army retaliated by targeting Pakistani military posts, killing fifty-five people. This retaliation led the Pakistanis to launch Operation Ghazab Lil Haq, which, according to Pakistani sources, killed more than 400 Taliban fighters and destroyed weapons and ammunition left behind by the Americans in 2021.It is doubtful that the force deployed by Islamabad will be sufficient to reduce the threats posed to Pakistan by the Taliban, the TTP, and IS-K. Such a shift in the balance of power is probably only conceivable if India does not intensify its relations with the Taliban. In the Iran war, the reshaping of alliancesWhile Karzai and Ghani’s closeness with New Delhi was one of the main reasons why Islamabad was calling for the return of the Taliban, the fact that the latter began to play the Indian card in order to better resist Pakistani pressure was seen as a betrayal by Islamabad. Afghan Foreign Minister Amir Khan Muttaqi and others during a meeting with Union External Affairs Minister S. Jaishankar (not visible in the picture) in New Delhi on October 10, 2025. Photo: PTI.In this regard, Afghan foreign minister Amir Khan Muttaqi’s visit to New Delhi in October 2025 represented a turning point: the skirmishes between the Afghan and Pakistani armies immediately took on new significance.In Pakistan’s interest, it is possible that third countries may intervene in this conflict. While Qatar, Saudi Arabia, the United Arab Emirates, and Turkey are natural candidates, China could also be a “friend in need.” With China coveting Afghanistan’s natural resources, the promise of economic development could lead Kabul to negotiate a modus vivendi with Islamabad.At the same time, we are now seeing a rapprochement between Pakistan and Saudi Arabia, which had distanced itself from Islamabad following Pakistan’s refusal to participate in the anti-Houthi coalition in 2015, among other reasons. Following the Israeli attack on Qatar on September 9, 2025, Pakistan and Saudi Arabia signed a defense pact. With this pact, Islamabad no longer needed to tread carefully around Tehran and can move closer to Riyadh without scruples.This dynamic is amplified by India’s rapprochement with the United Arab Emirates – with which New Delhi recently signed a defense agreement, just as the UAE was distancing itself from Saudi Arabia – as well as with Israel. Notably, before the start of the Iran war, on February 26 and 27, Narendra Modi made an official visit to Tel Aviv to sign new trade agreements and arms contracts.From now on, Pakistan can feel reassured about the risk of encirclement: due to the military operation led by Israel and the United States, this risk is lower – the two powers having also obtained India’s withdrawal from the Iranian port of Chabahar. But by giving Jaysh al-Adl new means to reinforce Baloch irredentism and separatism, the current situation could spread chaos to eastern Iran.This article draws from a French text, “L’autre guerre: le Pakistan et l’Afghanistan face au chaos iranien,” Le Grand Continent, March 5, 2026 and from my book, The Pakistan Paradox, (Penguin India). Christophe Jaffrelot is Senior Research Fellow at CERI-Sciences Po/CNRS, Paris, Professor of Indian Politics and Sociology at King’s College London, Non resident Scholar at the Carnegie Endowment for International Peace and Chair of the British Association for South Asian Studies.