Pakistan's objective interest in Central Asia is to secure it as a position of depth, for both the stationing of vulnerable military assets and the passage of military supplies, in the event of hostilities with India. During the 1965 Indo-Pakistan War, King Zahir Shah of Afghanistan permitted sanctuary for the civil aircraft of Pakistan International Airlines and the passage of supplies from Iran and elsewhere to Pakistan. Similarly, Pakistan's provinces of Balochistan and the Northwest Frontier Province (NWFP) provide reserve air bases and cantonments for some of its corps. This 'depth' is not a lateral communications system facilitating strategic redeployment due to the absence of developed infrastructure or a base for retreated forces, since by then Pakistan will have abandoned most of its population and industrial base.

Afghan-Pakistan relations are undermined however by the status of the Pakhtun people whose territory straddles the frontier and whose leaders have a decisive influence in Kabul (accounting for half of Afghanistan's thirty million people) and are second in their importance in Islamabad (after the Punjabis) where their population accounts for fifteen percent of Pakistan's population of 160 million. Pakistan's reluctance to grant concessions on the basis of principles of self-determination led to Afghanistan's refusal to recognize Pakistan at partition, Pakistan's retaliatory closure of third party trade for land-locked Afghanistan, and Afghanistan's military attacks from the late-1940s until 1963. Pakistan's basis of legitimacy is as the home for Muslims in South Asia, which has led the state to foster a pervasive ideology of Islam to cement together its disparate ethnic constituents.

Within this context, Pakistan's ideal interest of a supportive Muslim neighbor is unstable and would inevitably be undermined by its ongoing dispute over Pakhtunistan. Twice stable relations were achieved. After over ten years of military clashes along the Pakistan-Afghan border between 1947 and 1963 which culminated in a series of war scares involving Afghan military mobilization, Afghan King Nadir Shah succeeded in an abrupt policy shift that normalized relations with Pakistan. A number of ruinous trade cut-offs by Pakistan, and repeated mediation efforts by Egypt, Saudi Arabia and Iran, led Kabul to set aside its demand for immediate change to the status quo in Pakhtunistan. Reasonably good relations prevailed between 1963 and 1973 until an internal coup deposed the Afghan monarchy and threatened fresh hostilities with Pakistan which thereafter sponsored various Islamist movements to undermine the Kabul government. The second instance of good relations followed the seizure of Kabul by the Taliban in 1996 through to 2001. The latter regime did not acquiesce to Pakistan's goals of recognition of the Durand Line but it did eliminate official sponsorship of Pakhtun separatist activism.[3]

Taliban rule from 1996 neutralized anti-Pakistan agitation in Afghanistan but did so with obvious sponsorship from Islamabad. Though Pakistan could help the Taliban seize Kabul, they could not then get it to deliver recognition of the Durand Line. Pakistan is not currently in a position, given NATO's presence, to compel Kabul's compliance with its goals. Arguably, the cordial period of Afghan-Pakistan relations since 2001 has been made possible by the restraining effect of NATO's presence on Kabul's irredentist activism. The remaining periods are of Afghan-Pakistan hostility, involve limited military action, and characterize relations from partition in 1947 to 1963 and from 1973 until the establishment of the Taliban regime in 2001.

Pakistan's immediate strategy is to avoid transparent negotiations and to emphasize its lack of freedom of action for three reasons. First, it is fearful that direct negotiations with NATO or Afghanistan regarding the frontier sanctuaries could lead to consideration of self-determination for the Pakhtun and Baloch people there as a means of reducing the effects of Islamist influence. Second, Pakistan cannot obtain any concessions from Afghanistan as long as NATO is backing the Kabul regime. Third, Pakistan does not want to break the Islamist movement that is countering Pakhtun separatism. Pakistan's current Afghan strategy is therefore to play for time until NATO scales-back its commitment and Islamabad can more directly pressure Kabul.

The principal Pakistani political actors with interests in Afghan policy can be grouped twofold into the traditional ruling elite of Pakistan and the Pakhtun and Baloch ethnic minorities. As a corporate entity, the traditional political elite relies on Islam to suppress ethnic nationalism and leftists both within Pakistan and against its neighbors in India and Afghanistan.[4] This is also in part to co-opt religious groups since traditional Islamic organizations, such as Jamaat-i-Islami had opposed the creation of Pakistan.[5] These elites are also the proponents of Pakistan's strategic interests in Afghanistan (outlined above). This elite consists of the senior military leadership, federal bureaucrats, including many mohajirs, traditional Punjabi and Sindhi landowners and, more recently, the emerging manufacturing sector.[6] While often mischaracterized as westernized, the elite shares a technocratic perspective, meaning that Islam is pragmatically bent to fit the developmental, technical and diplomatic needs of the state.[7] In effect, Islamic Pakistan welcomes Western aid and trade, has unlinked its nuclear weapons program with any broader Islamic goal, and has secured close relations with 'atheist' China.[8] The July 2007 assault on the Islamist-held Red Mosque by the Special Services Group (SSG), the army's main commando force, in response to Chinese concerns is indicative of this commitment to technocracy. The business (and military) elite is primarily focused on local manufacturing and textile exports, and exerts no interest to improve trade with Afghanistan.[9]

The second grouping of interests is the ethnic minorities of the Baloch and the Pakhtun. The Baloch, a minority in their own province of Baluchistan, have traditionally benefited from Afghan support for their nationalist aspirations against what they perceive as Punjabi domination of Pakistan. In the past they have relied on Afghanistan for arms and sanctuary, though their relative influence on Pakistan's policy is very limited.[10] In contrast, the Pakhtun have substantial influence on Pakistan's Afghan policy. The Pakistani Pakhtun (numbering 35 million), whose ethnic kin constitute half of Afghanistan's population, can be sub-divided into two further groups.[11] The settled Pakhtun of the Northwest Frontier Province (NWFP) were traditionally over-represented in the British India Army and by the 1960s were over-represented among Pakistan's senior military elite (constituting 22-25 percent of the officer corps, as compared with 70 percent being Punjabi in the late-1970s).[12] While initially opposed to the formation of Pakistan and assertive in their national identity the Pakhtun of the NWFP have become strong supporters of Pakistan as they have developed economically.[13] A second grouping of Pakhtun are those that inhabit the autonomous tribal areas. They tend to share close relations with tribal members on the Afghan side of the border but they value their local autonomy more highly than either Afghan or Pakistan nationality. They have historically resisted incursions by both states. Conservative social values in both groupings of Pakhtun have set positive conditions for the support of Islamist movements, though marginally more among the tribal populations. Since the 1970s, the Pakistani state has encouraged Islamist political parties to counter-balance the strong nationalist aspirations in the NWFP.

Pakhtun interests are expressed through the nearly independent Afghan policy of the Inter-Services Intelligence (ISI), where the Pakhtun are also substantially over-represented (constituting between 30-40 percent of its personnel). The mainly ethnically Punjabi military has directed more than one purge of the ISI since the early 1990s to attempt to maintain control over it.[14] The ISI is also strongly supportive of Islamist agents based on its war experience in Afghanistan, Kashmir and against Shia and Baloch Pakistanis.[15] The result is that the Pakhtun-influenced ISI is interested in establishing an Islamist Pakhtun authority in Kabul regardless of the larger goals of the Pakistani state or the effects on its relations with NATO. A rational Pakistan policy would be one that sought a friendly Afghanistan, thereby reducing Kabul's support for separatist tendencies among the Pakistani Pakhtun. Since Pakhtun governments in Kabul inevitably need Pakhtun tribal support to counter-balance the Tajik, Uzbek, Farsiwans and Hazara Afghans, they inevitably seek to mobilize tribal support by scapegoating Pakistan and by declaring support for separatist Pakhtun within the tribal frontier.[16] Pakistan should therefore sponsor a non-Pakhtun regime in Kabul which would have no interest in mobilizing the Pakhtun.

This was precisely the policy of Pakistan Prime Minister Zulfiqar Ali Bhutto (a non-Islamist Sindhi) in 1973, when he supported a broad coalition of Islamists to counter the Kabul government, including Gulbuddin Hekmatyar (a Pakhtun), as well as Burhanuddin Rabbani and Ahmed Shah Massoud (both Tajik).[17] After the failure of an abortive uprising by Islamists in Afghanistan in 1975, the Pakhtun-dominated ISI favored Hekmatyar over the others and Afghan policy was thereafter distorted by Pakhtun rather than broader Pakistani or Punjabi-Sindhi interests.[18] Nevertheless, Pakistan President General Zia ul-Haq's strategy was to fragment Afghanistan rather than permit it to become united under an ethnically Pakhtun Taliban which occurred during the tenure of Benazir Bhutto's government in 1996.[19]

One tempting NATO strategy is the promotion of democracy in Pakistan to neutralize the supposed military influence that is driving the Islamist Afghanistan policy in Islamabad. However, the reintroduction of civilian-led government in Pakistan, whether a People's Party of Pakistan (PPP) shadowed by Asi Ali Zardari, or Nawaz Sharif's Muslim League (ML), both of which ruled in the 1980s and 1990s, will not likely produce a dramatic change in Pakistan's Afghan policy. Benazir Bhutto (of the PPP) was effectively sidelined in 1988 and 1989 when the ISI initiated operations in Kashmir and Sharif was perhaps aware but powerless to interfere with the Military Intelligence agency's (MI) operation in Kargil in 1999. Not since the period of 1971 to 1977 under Benazir's father, Zulfiqar Ali Bhutto, or near the end of Nawaz Sharif's last term months in office in 1999, were civilian leaders sufficiently strong to challenge the military in foreign policy. The conditions during the earlier period were the after effects of military defeat in East Pakistan that destroyed the public legitimacy of the army leadership. During the latter period, Nawaz Sharif was gradually co-opting the military's religious support base.[20] Pervaiz Musharraf has maintained the military's background influence on policy through his own presidential office, the National Security Council that is currently headed by him, and the military's intelligence agencies. The current conditions do not exist for the civilian political parties to challenge their exclusion by the military from Pakistan's Afghanistan policy.

Furthermore, periods of direct military rule in Pakistan are associated with stable relations with neighbors because the military is primarily concerned with healthy economic growth to maintain its defense budget rather than confrontation. Pakistan's foreign policy is most volatile during periods of hybrid civilian-military rule, either when declining military rule is incorporating civilian stakeholders to maintain its public legitimacy or when weak civilian regimes seek military support to remain in power. The 1965 and 1971 wars with India demonstrate the former and Pakistan's support to Kashmir in 1989 and the Kargil episode demonstrate the latter.[21] In both instances the normal civil-military decision-making process is circumvented by particularist interests, making an accurate assessment of any policy choice deficient.[22]

Was President Pervaiz Musharraf to suffer a sufficient drop in popularity that his military and traditional elite backers withdraw their support, leaving him in direct competition with the traditional civilian parties, then he may be compelled to seek support by propounding more extreme, perhaps Islamist, policies. Were a weak PPP or ML coalition emerge, they may come to rely on the same radical groups to offset or coopt military influence. In either case foreign policy would become diversionary and scapegoat foreign threats to sustain public legitimacy. It is particularly during these periods of hybrid rule that regional interests, in Kashmir and the NWFP, evade central control and assert independent local foreign policies, including military adventurism (as occurred in the 1990s in both Afghanistan and Kashmir). The most stable regime would therefore either be a direct military or strong civilian government.

Pakistan's elite fears that suppressing militant Islam would weaken the core ideology of the state, alienate key private backers in Saudi Arabia and the Emirates, prove costly in its enforcement, and irreversibly extinguish a ready reserve of holy warriors that have proved very useful for Pakistan's security against India and Afghanistan. Each of these issues is addressed in turn.

Pakistan depends on a mohajir-inspired nationalist Islam for legitimacy and to counterbalance centrifugal ethnic sentiments as well as to shield the underlying ethnic nature of the essentially Punjabi-run state.[23] To counterbalance emerging leftist movements in the 1970s and Shia activism of the 1980s the military incorporated conservative (rather than radical) religious representatives within its governing structure.[24] Pakistan is approximately 80 percent Sunni. The remainder, including the founder of Pakistan, Mohammed Ali Jinnah, is Shia. Most Pakistanis are Hanafi Sunnis, though the Barelvi tradition of saint-worshipping common among 15 percent of the Sunni population is practiced by a majority of Pakistanis.[25] The Barelvis are opposed by the more fundamentalist Hanafi Deobandi, who also constitute 15 percent and the primarily Gulf-funded Wahhabists and Salafists.[26] Poverty and lack of state capacity explains to some extent the increased prominence of religious schools (madrassas), most of which preach non-violence, as well as their radicalization away from Urdu arts and towards Deobandi, Salafist and Wahhabist teaching.[27] While the Deobandi movement which was the primary ideological influence on the Taliban was founded as a reaction to British occupation in 1867, it (and the Salafists) had no history of radical militancy prior to deliberate ISI encouragement during the Afghanistan war against Soviet occupation.[28] Despite the disruptive increase in Islamist terrorism in Pakistan as a result of its support for militant Islamist groups, it is not clear that this would not have been caused anyway by the scale of Gulf funding directed at Pakistan following the Iranian revolution. [29]

The Pakistan military, as well as the Muslim League and other parties that have had close political association with clerics, are reluctant to undermine Saudi diplomatic and financial support by blocking private funding of Deobandi, Wahhabist and Salafist religious movements in Pakistan and Afghanistan, particularly the Taliban.[30] The degree of Saudi influence is demonstrated by the fact that Pakistan sought their permission before detonating its nuclear device. However, it should be highlighted that a great deal of Islamist funding also has its origins in the westernized diaspora.[31] This pressure from Saudi Arabia has not however inhibited Pakistan from blocking jihadists from deploying into China's predominantly Muslim province of Xinjiang.[32] This suggests that Pakistan is certainly in a position to suppress some of the aspirations of its Islamist groups, given sufficient incentive.

Pakistan's passivity is also reinforced by the cost of an intervention of sufficient scale to dominate the tribal areas, which in its worst manifestation, could result in the equivalent of the 1897 Great Tribal Revolt that preoccupied the British.[33] Militarily suppressing the Taliban may provoke the Pakhtun, given the difficulty of disentangling tribal from religious sentiments in the Federally Administered Tribal Areas (FATA) and inflame areas within the NWFP. [34] Furthermore, any intervention would likely have only a marginal effect on the strength of the Taliban given the importation of weapons from Central Asia and reliance on Afghan drug production.[35]

As long as Afghanistan retains the possibility of encouraging a secessionist revolt among the Pakistani Pakhtun tribes with which it maintains contact, Pakistan has an incentive to preserve an Islamist counter-balance.[36] One Pakistani concern is that if the Islamists are suppressed they may not only be supplanted by Pakhtun nationalists but they may be more difficult to resurrect. Among the Pakhtun in particular, Pakhtunwali culture has traditionally been more influential than Islam, and Taliban successes in pushing Salafist tenets among the Pakhtun were transient.[37] During the Afghanistan War, to avert a subsequent Pakhtun uprising, the ISI resisted the CIA's policy of widely distributing weapons and instead channeled the weapons to seven primarily Islamist groups that were still never reliably under Pakistan's control.[38] Currently most tribal Pakhtun leaders support a form of Pakhtun autonomy within Pakistan (Pashtunkwa), but there are nevertheless substantial tribal factions that have pretensions towards an independent Pakhtunistan.[39]

Some have suggested a grand bargain in which Afghanistan, along with key Pakhtun political parties, would recognize the Durand Line in exchange for Pakhtun autonomy within Pakistan and an open border concept, as well as guaranteed trade and transit access to the Indian Ocean. In this scenario China would be encouraged by the United States to prod Pakistan into agreement.[40] This proposal is unlikely for three reasons. First, the US does not have the necessary influence and neither Saudi Arabia nor China has the interest to pressure Pakistan into conciliation with Afghanistan. Second, Afghanistan is too unstable to provide convincing treaty commitments to Pakistan, especially in promising not to stoke secessionism. Third, Pakistan recognizes that NATO's interest in Afghanistan is weaker than its own interest and it is just a matter of time before NATO's resolve weakens.

The normalization of Afghan-Pakistan relations in 1963 was attained by coercive sanctions and threats of military punishment (in 1959 Pakistan had claimed that it could seize Kabul in a few days).[41] Pakistani threats to use military force in the present are likely to provoke a strong counter-threat by NATO. Furthermore, if Pakistan was to carry out any ground force-delivered punitive attack on Afghanistan, except from routes near Quetta and Peshawar, it would be substantially delayed and weakened by the need first to pacify the tribal belt to secure its supply lines. Air attacks are also unlikely given Pakistan's decisive weakness in this area compared to NATO, which can deploy substantial naval air power in the Gulf and the Arabian Sea. Pakistan would be aware that security guarantees from China would not be valid under these circumstances. Arguably Pakistan's interdiction of Afghan transit trade remains an effective threat because NATO has not yet adopted policies seeking to resolve the trade impasse. However, the low salience of the trade issue may also be because Afghanistan's legitimate trade activity is below what it was during the mid-twentieth century, when trade embargos had more substantial impact. So Pakistan's most effective option is a do-nothing strategy, which imposes a cost on the Kabul regime, provides plausible deniability to the Islamabad government regarding the actions of Pakhtun insurgents operating from the frontier area, and provides a force-in-being for future intervention.

So what are NATO's options? NATO's goal of developing Afghanistan sufficiently to manage its own domestic security (with external funding) to standards of the 1960s is perhaps a decade off, especially if it continues along its relatively tempered developmental plan. Since the nineteenth century, Kabul has never been able to maintain internal order without external financing.[42] Afghanistan's ability to manage its external threats is forever beyond its reach given the relative size of its neighbors and is dependent entirely on alliance security currently provided by NATO. NATO has few non-escalatory military options. Inviting greater Indian participation, re-routing trade through Iran, pushing the self-determination of the Pakhtun or Baloch people, or engaging in assorted uninvited cross-border activity (ground reconnaissance, air strikes, or ground raids) will likely provoke Pakistan to retaliate through its agents in Afghanistan. Consequently, direct cross-border occupation will almost certainly be met with limited army resistance. NATO has two remaining venues of influence. First, NATO's presence acts as a restraint on Afghan provocation of secessionism, thereby satisfying one of Islamabad's goals. Second, NATO could offer positive trade and aid incentives to Pakistan to very gradually withdraw its support to those elements of its society that foment Pakhtun insurgency in Afghanistan (and Pakistan). The long-term effect of such a strategy would be a gradual economic integration and normalization of the Afghan and Pakistan frontier areas, reinforced by NATO's restraint against any irredentist temptations in Kabul.