A recent poll suggests that half of Pakistan’s population believes that Pakistani strongman Pervez Musharraf, or military leaders very close to him, had something to do with the assassination of Benazir Bhutto. Pakistan may be the world’s center of wacky conspiracy theories, but this public perception should not be lightly dismissed. In fact the Pakistani military and its intelligence arm have deep ties in to the Islamic militants who considered Bhutto their greatest threat on the Pakistani political stage.

For those trying to make sense out of the tremendously complex, and tremendously important threads in Pakistan and Afghanistan that tie together Musharraf, the Pakistani senior military establishment, Pakistan’s Interservice Intelligence (ISI), the Taliban in both Pakistan and Afghanistan, tribal chiefs and groups, and various terrorist groups which float in the shadows between all of these players, Carlotta Gall and her colleague David Rohde offer an important contribution in today’s New York Times.

I first met Gall more than ten years ago when she was working for the BBC covering Central Asia. Even then she was a very rare figure, a Westerner who tenaciously dug in to learn what was going on. Gall never thought the answers were to be found in the lobbies of the Sheratons and Intercontinentals, which is where the bulk of the press corps seem to hang out to pick up their scoops. She went to the villages and small towns to form a solid picture of the situation and she probed insistently into the shadowy world of the Pakistani intelligence service and its various cat’s paws.

Her article today gives one of the best accounts of the relationship between ISI and their radical agents, and the ambiguity of much of this relationship. It’s mandatory reading.

Pakistan’s premier military intelligence agency has lost control of some of the networks of Pakistani militants it has nurtured since the 1980s, and is now suffering the violent blowback of that policy, two former senior intelligence officials and other officials close to the agency say. As the military has moved against them, the militants have turned on their former handlers, the officials said. Joining with other extremist groups, they have battled Pakistani security forces and helped militants carry out a record number of suicide attacks last year, including some aimed directly at army and intelligence units as well as prominent political figures, possibly even Benazir Bhutto.

The growing strength of the militants, many of whom now express support for Al Qaeda’s global jihad, presents a grave threat to Pakistan’s security, as well as NATO efforts to push back the Taliban in Afghanistan. American officials have begun to weigh more robust covert operations to go after Al Qaeda in the lawless border areas because they are so concerned that the Pakistani government is unable to do so. The unusual disclosures regarding Pakistan’s leading military intelligence agency — Inter-Services Intelligence, or the ISI — emerged in interviews last month with former senior Pakistani intelligence officials. The disclosures confirm some of the worst fears, and suspicions, of American and Western military officials and diplomats.

The ISI is the critical prop to Musharraf’s reign. It was responsible for his rigged election successes in the past and certainly will play the same role in the coming election. The Times piece goes on to offer specific detail on an internal review of the agency and its relationship with radicals, which leaves many asking who is guarding whom?

Barney Rubin goes on to link this report with the alarming bombing attack on Kabul’s luxury Serena Hotel.

The attack on the Serena Hotel in Kabul is a shock for all of us foreigners who have gone there for tea. Conferences, or brunch, even if we never stayed there. Like most people who go in and out of the Kabul expatriate community, I imagine, I knew a couple of people who were there — in my case including some Norwegian diplomats. News reports mention that this was Afghanistan’s only “five-star” hotel. They don’t mention that nearly all Afghans live in “zero-star” conditions, including the thousands of people who pass that traffic circle every day and see inaccessible luxury behind thick walls. The rioters attacked the Serena in May 2006, apparently believing that alcohol is served there, though it is not.

I am sure that the people of Kabul don’t want more violence in their city. They were badly frightened by the riots in 2006. But there is huge resentment and anger building up at the overbearing foreign presence. The May 2006 riots were sparked by an accident where US military vehicles killed a pedestrian. Afghans see and often do not distinguish among the “Chinese restaurant” brothels and the glittering restaurants (by Afghan standards, not ours) serving luxuries, including alcohol, to foreigners, some of whom are being highly paid to destroy Afghanistan’s opium livelihood, which Afghan Islamic figures say is no worse than the alcohol they drink at night after destroying farmers’ poppy crops.

So, no ambiguity here: Westerners are now being targeted, and the Taliban’s reach is right into their ultimate luxury sanctuary in Kabul. This development opens the year in Kabul on an appropriate note of alarm. Afghanistan is not Iraq, and the prospects for success of the Western effort there are considerably higher than in Iraq. The stakes are also higher, I believe. This is the challenge at center stage of the current conflict: the amorphous borderlands between Pakistan and Afghanistan, the ultimate growth matrix of the terrorist threat that manifested itself on 9/11, and which is, six years later, stronger than ever.