In the last few weeks, Pakistani and American intelligence forces have arrested at least fourteen Taliban leaders in Pakistan. These arrests were carried out with some reluctance by Pakistani intelligence personnel, but were apparently ordered by the commander of the army, who was backed by the civilian government, which had recently purged the intelligence agencies of many Islamic radicals. Pakistan has turned away from its creation. Pakistan has destroyed much of the Pakistani Taliban in the last six months, and is now arresting the leadership of the Afghan Taliban.
Pakistani intelligence officials have good reason to be unhappy with this roundup. Even though Pakistan won't allow the Taliban leaders to be interrogated alone by the Americans, much less taken out of the country, U.S. officials have been able to sit in. That quickly revealed that the Taliban leadership had long been in touch with Pakistani intelligence, and some of the captives were quite indignant at how this long (nearly two decades) relationship had been so unceremoniously ended.
The ISI (Inter Service Intelligence agency, sort of a Pakistani CIA, run by the military) has long insisted that staying in touch with the Taliban, and other Islamic radical outfits, helped protect Pakistan, and contribute to Pakistani foreign policy efforts. It hasn't worked out that way, especially after September 11, 2001. Back then, Pakistan was forced to make a choice; either join the United States in a war against Islamic terrorism, or go to war with the United States. That was a no brainer, but ISI tried to maintain its relationships with Islamic radical groups. That didn't work out too well.
This was all part of a trend. For several years now, the United States, Afghanistan, India and many Pakistanis, have been pressuring the Pakistani government to reform the ISI. This organization has long been a power unto itself, with its own agenda and many members who support Islamic radicalism. Two years ago, the government sought to disband the political wing of the ISI. This section was believed be largely responsible for Pakistani support of Islamic, or simply Pakistani, terrorist operations in Afghanistan and India, as well as support for Taliban and al Qaeda in Pakistan itself. The political wing has also served as a domestic spying operation whenever the military was running the country (which is more than half the time.) Pakistan is currently run by a civilian government that came to power in the Summer of 2008.
ISI has long supported Islamic terrorists, but now Pakistan is determined to root out "Taliban spies" in the ISI. The problem is that these Islamic radicals have been operating openly in the ISI for three decades, and were put there by the government in the late 1970s, when it was decided that Islamic conservatism was the solution for Pakistan's problems (corruption and religious/ethnic conflicts.) These guys are not just "Taliban spies," but Pakistani intelligence professionals that believed, and encouraged (they invented the Taliban) Islamic radicalism.
The ISI itself was created in 1948 as a reaction to the inability of the IB (Intelligence Bureau, which collected intelligence on foreign countries in general) and MI (Military Intelligence, which collected intel on military matters) to work together and provide useful information for the government. The ISI was supposed to take intel from IB and MI, analyze it and present it to senior government officials. But in the 1950s, the government began to use the ISI to collect intel on Pakistanis, especially those suspected of opposing whatever government was in power. This backfired eventually, and in the 1970s, the ISI was much reduced by a civilian government. But when another coup took place in 1977, and the new military government decided that religion was the cure for what ailed the country.
Typically, the Pakistani generals seized control of the government every decade or so, when the corruption and incompetence of elected officials became too much for the military men to tolerate. The generals never did much better, and eventually there were elections, and the cycle continued. The latest iteration began in 1999, when the army took over, and was only forced, by public pressure, to relinquish power two years ago. Civilian governments tend to be hostile to the ISI, and apparently this produced a serious effort to clear out many of the Islamic radicals.
The ISI grew particularly strong during the 1980s, when billions of dollars, most of it in the form of military and economic aid, arrived from the oil-rich Arab governments of the Persian Gulf. All this was to support the Afghans, who were resisting a Russian invasion (in support of Afghan communists who had taken control of the government, and triggered a revolt of the tribes). The Afghan communists were atheists, and this greatly offended Saudi Arabia, and other Arab countries, who feared that Russia would encourage Arab communists to rebel elsewhere. So the resistance to the Russians in Afghanistan was declared a holy war which, after a fashion, it was. After about nine years of fighting the tribes, the Russians got tired of their slow progress (and had more pressing problems back home, like the collapse of their economy from decades of communist mismanagement), and left.
The Russians were gone by 1989 (and the Soviet Union collapsed two years later), but the Afghans promptly fell upon each other and the civil war seemed never-ending. This upset Pakistan, which wanted to send millions of Afghan refugees back home. Few of the refugees were interested as long as Afghans were still fighting each other. So the ISI created its own faction, the Taliban, by recruiting teachers and students from a network of religious schools that had been established (with the help of Saudi Arabian religious charities) in the 1980s. The most eager recruits were young Afghans from the refugee camps. The Taliban were fanatical, and most Afghans were willing to support them because they brought peace and justice. But the Taliban never conquered all of Afghanistan, especially in the north, where there were few Pushtun tribes (most Taliban were Pushtuns, from tribes in southern Afghanistan). The Pushtuns were about 40 percent of the population, and had always been the most prominent faction in Afghanistan (the king of Afghanistan was traditionally a Pushtun.)
Although a military junta was again running Pakistan when September 11, 2001 came along, the president of the country, an army general (Pervez Musharraf), sided with the United States, and turned against the Taliban. But many in the ISI continued to support the Taliban, and the army was too dependent on the ISI (for domestic intelligence, and to control Islamic militants that were attacking India, especially in Kashmir) to crack down on this ISI treachery.
Al Qaeda took this betrayal badly, and declared war on the Pakistani government. The ISI was used to seek out and kill or capture most of the hostile al Qaeda operatives in Pakistan. But the ISI told Islamic terrorists who remained neutral that they would be left alone. The ISI thwarted government efforts to have the army clear al Qaeda out of the border areas (populated largely by Pushtun tribes, there being more Pushtuns in Pakistan than in Afghanistan). But now, in one sense, it's September 11, 2001 all over again. The U.S. has told Pakistan that it is fed up with getting screwed around by the ISI, and if Pakistan doesn't clean out the ISI, and shut down Islamic terrorists along the Afghan border, NATO, U.S. and Afghan troops will cross the border and do it.
Pakistan wants continued U.S. military aid to bolster its defenses against India. But if it suddenly has a hostile U.S. in Afghanistan, and less (or no) military aid, its general military situation will be, well, not good. While Afghanistan, and the foreign troops there, are dependent on Pakistani ports and trucking companies for supplies, Pakistan is also dependent on the U.S. Navy for access to the sea. Pakistan does not want to go to war with the United States in order to defend Islamic terrorists it openly says it is at war with. Pakistan is being forced to destroy the Islamic radical movement it has nurtured over the last three decades, although it's still questionable if there's enough political will in Pakistan to actually do the deed. ISI critics also call for more police, and more professional and better equipped ones at that. The U.S. is threatening to restrict aid if the Pakistanis do not reform the police and ISI.