I can't speak for the nation obviously, but among virtually everyone I knew in 2007 it seemed obvious that at least part of the Pakistani government was playing a double game. Of course it's entirely possible that this is the smallest tip of a much greater iceberg of ISI/Pakistani military duplicity.

The current wave of Pakistan-bashing is not without a reason. There are plans to discredit Pakistan and create enabling environments for India to take over Afghanistan after the US departure. Pakistan has been used beyond its capacity and its services are no more required by the US. As against allegations that ISI has contacts with Haqqani Network fighting NATO forces in Afghanistan, RAW has contacts with Tehreek-e-Taliban Pakistan (TTP) fighting Pakistani state in Swat, South Waziristan and elsewhere in the tribal region. RAW is many steps ahead of ISI in this respect. It is fanning and fuelling insurgency in Balochistan and FATA and is funding and actually equipping TTP and Baloch insurgents. Some target-killers arrested in recent Karachi unrest confessed to have received training from RAW. No wonder, some call Tehreek-e-Taliban Pakistan as Tehreek-e-RAWliban Pakistan. Some pundits argue that Haqqani network, based in North Waziristan, has never attacked an official target in Pakistan - further evidence of its collusive relationship with that country's security services. When their struggle is focused on fighting foreign occupation forces and their collaborators including India, why should they insist the network attack Pakistan which has no role in Kabul? By this flawed logic, TTP fighting Pakistan and having killed 35000 civilians and 3000 security personnel provide collusive relationship with RAW and CIA. And mind you, this fight is taking place right inside Pakistan. By all definitions, TTP and Baloch insurgency is proxy war being fought by RAW inside Pakistan. Major objectives of this proxy war are keeping Pakistan away from Afghanistan to give India decisive role in Kabul, keeping China away from Gwadar-China energy corridor and depriving Pakistan from natural resources of Afghanistan. Read more at: http://pksecurity.blogspot.com/2011/09/pakistan-bashing-prelude-to-deliver.html

"Second, the incident also shows you the dangers that arise when governments keep lots of secrets. Suppose this story had come out back in 2007."

The story was out in 2007, for example here: http://www.monstersandcritics.com/news/southasia/news/article_1305180.php/Thousands_protest_Afghan-Pakistani_clashes_Roundup, and there is nothing new in the NYT piece.

Also please note paragraph 35 of the 36 paragraph long NYT piece. Two U.S. generals there are confirming the original story of 2007.

This was a pure anti-Pakistan propaganda piece the NYT put on page one. There was nothing new in it at all.

I don't like this chain of events one bit. If the story was leaked on purpose (which seems likely), the government has obviously decided to deliberately harm US-Pakistani relations even further. The incident got no or low (thank you Moonofa) coverage, so no harm could have been done if the government just let sleeping dogs lie for a little longer, until the withdrawal from Afghanistan finally happens.

This is a signal of shifting policy. With no end in sight for the Afghan war, the Obama administration has decided to gamble. They hope to score political capital before the elections, as from now on, Obama will avert all criticism of his Afghan policy by pointing the finger at Pakistan. Meanwhile they hope that the military aid package is enough to bribe Pakistan into swallowing every single insult. The gamble gets interesting when the Pakistani leadership decides that its credibility and internal stability is worth more than the aid package, which is unlikely unless the US decides to withhold or terminate the aid, which it threatens to do. In that case, the gamble is lost, the US cannot conquer and control Pakistan whilst maintaining its commitment in Afghanistan.

Bottom line: we may see stories like this, and more threats to Pakistan as the elections are drawing near, but real action (like cancellation of aid) is unlikely to follow. What I fear is that 1. a more jingoistic US government may cancel the aid, forfeiting the gamble, triggering the closure of Pakistani borders, 2. the not-so-considerate generals may decide they had enough, again closing the borders. With tens of thousands of Americans still in Afghanistan, this would leave the US little choice but to attack Pakistan. Well, the US tends to resort to violence even in the presence of alternatives anyway. That war would be a catastrophe.

On a side-note: how about the Pakistani civilians/soldiers/officers killed by the American military?

US has finally met the real enemy in Afghanistan!

Wow! It turns out to be America’s primary ally in its fight against terrorism as well.

But then America has known all along the duplicitous game that Pakistani State has been playing since 2001. Bush administration just consciously decided to keep it under wraps after forcing Pakistan to join America’s fight under the threat of ‘bombing Pakistan to stone age if Pakistan refused’ by Richard Armitage in 2001.

The seeds of the ‘current Afghan tragedy’ were sowed in Washington when Bush administration decided to allow Musharraf to spirit away by airlift hundreds, if not thousands, of Taliban operatives cornered by the advancing Northern Alliance in Kunduz in November, 2001. Pakistan relocated those Taliban cadres including Mullah Mohammed Omar to Quetta, the provincial capital of Baluchistan (now relocated to Karachi by Pakistani ISI to protect them from possible US drone attacks) and Haqqani network (HQN) to North Waziristan from where Mullah Omar’s QST and Haqqani’s HQN have been planning raids in Afghanistan ever since.

U. S. has deliberately deluded itself about Afghan Taliban’s Pakistani connections in fueling and sustaining Afghan insurgency as reported by Matt Waldman in ‘The sun in the sky‘ on 6/13/2010, corroborated by WikiLeaks leaks on 7/25/2010 and then further corroborated by Chris Alexander, Canadian ambassador to Afghanistan from 2003 to 2005 and Deputy Special Representative of the UN Secretary-General for Afghanistan from 2005 until 2009 in his article on 7/30/2010 titled ‘The huge scale of Pakistan‘s complicity‘.

Duplicitous Pakistan has U. S. under the barrel of a gun - US can NOT use its aid leverage to force Pakistan to stop supporting terrorist groups who kill US/NATO troops in Afghanistan day in and day out since 2001 because US needs Pakistan’s help in ferrying supplies to those very US/NATO troops.

U. S. deserves to be duped by Pakistan for intentionally ignoring Pakistani State’s double game of running with the ‘terrorist hares’ while hunting with the ‘American hounds’.

is news? There is nothing that Pakistan has done in the last 10 years that is inconsistent with its national interests. It backs the US because we threatened them. It backs the Taliban because it wants the future Afghanistan government to be their allies.

This is no more duplicitous than Nato getting a UN mandate to protect civilian lives and using it as an excuse for regime change, to just give one example among thousands.

Mr Walt's distinction between what the military want out of Afghanistan & Pakistan, and what the civilian administration wants -- this latter representing the American people -- is possibly the most important of this article. It's been clear for some time that the civilian administrations, Bush and Obama alike, have been less in touch with military aspirations than seems good for the nation, and that the military on some occasions in the past half-dozen years have on occasion flirted with deceiving or disregarding the principle of civilian control to the best of their ability.Both sides seem happy to keep important information away from the taxpayers, to help execution of their plans.

As to Pakistani military loyalties, I refer to a story widely published in 2001 to the effect that a brigadier was sent to Kabul in the first days or the US air campaign against the Taliban government to advise them to comply with whatever the Americans wanted. Instead, he went rogue, disappeared, and started giving the Taliban tips on how to protect themselves from aerial attack. Were these reports fictional? Or has this warning embarrassment been deep-sixed because it didn't fit in with Bush and military dreams of what was possible in Afghanistan?

The head of Pakistan's ISI is approved by our own DNI. I would suggest that the double game is being played on us, not the US intelligence agencies, US military or even our Congress critters. This is open duplicity on the part of all three. Pakistan is protecting its interests, the US is working counter to our I interests, all in the name of bureaucratic self preservation.