Gen. David Petraeus forged extremely good relations with Pakistan’s armed forces. Will his ambitious strategy in Afghanistan destroy that goodwill, and with that mess up the U.S. endgame?

Islamabad -- Hundreds of NATO cargo trucks and containers are back on Pakistani roads, carrying vital military, fuel, and food supplies destined for troops based in Afghanistan. These thousands of kilometers of roads between the Karachi port in the south and the northwestern and southwestern border towns Torkham and Chaman remain the key link in this crucial supply chain, and the closure of Torkham halted some 6,500 trucks.

This supply chain came to a grinding halt after NATO helicopters fired missiles on a Pakistani security post in the tribal region of Kurram on September 30, destroying the post and killing two soldiers on the spot.

Pakistan reacted fiercely to the border incursion, closing down the border in the northwest to protest both the killings and the border violation. Also, within the next few days, NATO lost almost 150 oil tankers at various locations, apparently to Taliban militants, who, too, grounded their torching of the trucks and containers to NATO’s incursion in Pakistan and to the drone strikes which continue to hammer their strongholds in North Waziristan.

Background interviews with a few of the most influential and senior-most Pakistani military commanders reveal that the altercation triggered unusually stiff opposition by the army chief General Ashfaq Kayani, who took up the deaths of his soldiers with Prime Minister Yousuf Raza Gilani in early October. The Pakistani military’s General Headquarters also conveyed its stringent disapproval of border infringement through the Office of the Defense Representative in the U.S. embassy in Islamabad to Adm. Mike Mullen, the chairman of the Joint Chiefs of Staff.

Viewed against the hard line that the Pakistani Army took on the issue of NATO supplies, it is safe to conclude that the resumption of the traffic through Torkham came at a relatively heavy cost, and caused quite a few ripples and ruptures in the U.S.-Pakistan military-to-military relationship that began two summers ago.

The honeymoon between the top military bosses of Pakistan and the United States began on board the USS Abraham Lincoln in the Indian Ocean in the summer of 2008, when General Ashfaq Kayani, accompanied by two aides, sat across the table to discuss his operational plans and limitations with five top American military officials including Admiral Mullen and Gen. Petraeus.

Both sides, according to Gen. Kayani, heard each other out, and this laid the foundation for a relationship that seemed to reach its apex in December last year, with the two American generals showering praise on General Kayani during their visits to Pakistan.

"I couldn’t give the Pakistani Army anything but an 'A' for how they’ve conducted their battle so far [in Swat and Waziristan]," Adm. Mullen told journalists accompanying him on December 16, 2009. "[Gen. Kayani] planned well, and he's been very deliberate about how much he can get done and when he can get it done," Mullen said, according to one correspondent. "I think that’s a very realistic approach to the operations."

At the center of today’s controversy between Pakistan and the United States stands the man who, along with Admiral Mullen, helped shape what many viewed as an unusual friendship between the two militaries: top U.S. and NATO commander in Afghanistan Gen. David Petraeus. Pakistani military officials, who once revered General Petraeus as a talented strategist, are wary of what they call his "ambitious plans" for the Af-Pak region. "We think we have checkmated Petraeus and thwarted his designs to impose a new hot pursuit paradigm on us," a senior Pakistani military official explained to me, amidst the backdrop of border violations by NATO choppers.

Some officials in the Pakistani Army believe Gen. Petraeus deliberately sent his men into hot pursuit of suspected Taliban fighters. With this, he may have wanted to gauge the Pakistani reaction before intensifying the U.S. military campaign into Waziristan, which U.S. military officials say is the source of at least 50 percent of attacks in Afghanistan.

Although public apologies from the Obama administration and Admiral Mike Mullen, chairman of the Joint Chiefs of Staff, paved the way to the resumption of cargo traffic across the Afghan border after eleven days, the incident, following another boots-on-ground operation in early September 2008 in South Waziristan, has dented the cordiality that had existed between Gen. Kayani and Gen. Petraeus and Mullen.

"We were left with no choice but to convey that the U.S. and NATO cannot take anything for granted, and we already are paying a very heavy price for our cooperation with the Western forces," the official said.

It was Mullen who went public in regretting the strikes by NATO helicopters and said he hopes to "avoid recurrence of a tragedy like this," but, highly placed government officials insist, Petraeus has already done the damage, though he too offered his public condolences.

The Pakistani Army and other concerned ministries, officials claim, are now insisting on reviewing the rules of engagement that have governed U.S.-Pakistan military cooperation since 2001.

They say that right-wing opposition parties and religio-political groups are already up in arms against the government because of the ongoing CIA-operated drone strikes into the Waziristan region -- more than 30 since early September -- and Taliban insurgents are attacking targets in southern and central Pakistan as well, and the country is reeling under the consequences of devastating floods.

Army and government officials believe that the country already is paying a heavy price and cannot put up with the ambitions of Gen. Petraeus, which are likely to have long-term implications for Pakistan.

That is why, it seems, the Pakistani government and the army are also concerned about the seeming American desperation to woo key Afghan insurgents into talks via Saudi Arabia, which wields considerable influence over important Afghan insurgent leaders such as Mullah Omar, Gulbuddin Hekmatyar, Professor Sayyaf, and some Kandahari businessmen who had allegedly also been friends with Mullah Omar.

For the Obama administration, opening up space for talks holds the key to what some analysts call the 'endgame.' But this phrase raises alarm in Pakistan.

It may be the endgame for the U.S. and NATO, but not for Pakistan. For Pakistan, it is a battle for long-term survival as a permanent neighbor of Afghanistan, a highly placed general says. He believes Gen. Petraeus shall have to lower his goalposts if he wishes to see some semblance of peace in Afghanistan.

"We shall have to find a mutually beneficial way -- not to the exclusion and detriment of Pakistan -- to marry the short term American objectives with our long time interests. We are here to stay next door to Afghanistan, unlike the Americans and other NATO members. They should try to understand it can’t be an endgame for us," the general insisted.

And near history is probably a good guide to follow that advice: an over-ambitious and reckless Pakistan and a disinterested America ignored the importance of an endgame after the Soviet withdrawal from Afghanistan in 1989. Both allowed warring Afghan factions to fight it out among themselves, rather than helping them put a power-sharing mechanism in place. The result: Afghanistan descended into factionalism and chaos. It now threatens Pakistan too.

Imtiaz Gul heads the Centre for Research and Security Studies, Islamabad and is the author of The Most Dangerous Place (Viking Penguin USA).