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It’s impossible to separate the crisis in US-Pakistan relations, which now threatens the Obama administration’s entire timetable for winding down the war by 2014, from the recent flap over an effort by some members of Pakistan’s civilian government, including ex-Ambassador Husain Haqqani, to enlist American support in blocking a military coup in Islamabad. Ad Policy

Let’s look at the pieces of the story.

First, Pakistan has announced its intention to withdraw from the December 5 conference in Bonn, Germany, that was created as a forum to build an international consensus about ending the war through a political accord that involved negotiating with the Taliban and its main sponsor, Pakistan. According to some reports, officials from the Taliban movement were to have been present on the sidelines of the meeting in Bonn, and then United States has spent much of 2011 seeking to open a dialogue with the Taliban. Because Pakistan is the chief backer of the Taliban, which it sees as its guarantor of a long-term presence in that country, Pakistan’s boycott of the Bonn meeting is potentially devastating to the idea of a political accord in Afghanistan.

Second, Pakistan has shut down the critical border crossings that the United States and NATO utilize to resupply the war effort. Without them, the NATO project is doomed. And Pakistan has also told the United States to remove its drones from the not-so-secret air base inside Pakistan, which will undercut, if not cripple, the counterproductive and bloody Predator and Reaper drone assaults on Al Qaeda, Taliban and allied targets in Pakistan’s tribal areas, especially in South Waziristan.

It’s not likely that Pakistan’s response to the killing of twenty-five soldiers by a NATO air strike on a border post is simply a reaction to that event. Pakistan’s military—which created, armed and trained the Taliban, helped install them in Afghanistan in the mid-1990s, protected Al Qaeda (including Osama bin Laden) and backs the Haqqani and Hekmatyar terrorist groups that are responsible for horrific acts of assassination, suicide bombings and such high-profile acts as the assault against the Indian embassy in Kabul—has long been chafing at the US presence in Afghanistan. Pakistan’s army sees the US occupation of Afghanistan as a direct threat to Pakistan’s fundamental interests there, and the more radical-nationalist and Islamist elements of the military see the United States as having designs on Pakistan’s nuclear arsenal as well. Until now, Pakistan and its ISI intelligence service have been content to keep Afghanistan on a low boil, awaiting the inevitable defeat and withdrawal of NATO. Now, it seems, the clandestine army junta that rules Pakistan from Rawalpindi might be ready to escalate the war.

Now let’s revisit the “Haqqani affair.”

Ambassador Haqqani is a long-time opponent of Pakistan’s military and of its Islamists. (His book, Between Mosque and Military, lays out the sad story of the army’s infatuation with hard-core Islamist militants going back to the 1970s and the rise of General Zia ul-Haq, the murderous dictator who hanged his predecessor, Zulfikar Ali Bhutto, and imposed a benighted version of Islam on Pakistan. (That was fine for the United States when, in the 1980s. Washington backed Zia in the jihad, pouring billions into the pockets of people like Haqqani and Hekmatyar.) I know from personal conversations with Ambassador Haqqani (no relations to the bloody Haqqani gang led by Jalaluddin and Sirajuddin Haqqani) that the ambassador is a true moderate and democrat, and several years ago, when he was a professor at Boston University, Haqqani invited me to make a presentation to his department on my book Devil’s Game: How the United States Helped Unleash Fundamentalist Islam.

After the killing of bin Laden, the Pakistani army was rumbling about making a coup d’état against Pakistan’s weak and corrupt civilian government, led now by President Asif Ali Zardari, who was married to the murdered political leader Benazir Bhutto, the daughter of the hanged former president. Apparently, though details are murky, Ambassador Haqqani and Zardari not only sought American help to forestall the coup but they promised to reform and remake Pakistan’s foreign policy in a radically different direction. They planned to oust the chief of staff and the head of the ISI, replacing them with anti-Taliban actors, and to launch a true campaign to uproot the Taliban from its protected headquarters in Quetta and go after its allies Haqqani and Hekmatyar. When the story was revealed, Haqqani resigned.

There’s no doubt that the Pakistan army is enraged over the reported Haqqani-Zardari countercoup plot. They’ve been angered by a steady stream of actions and accusations by the Obama administration for more than a year: the January killings of Pakistani operatives by a CIA officer, the killing of bin Laden, cross-border drone strikes, the charge by the chairman of US Joint Chiefs of Staff that Haqqani’s gang was a “veritable arm” of the ISI and—worst of all, by far—the deaths of the twenty-five soldiers at the border this week. Now, it appears, the military is making its move to hit back.

The United States needs to get on its knees and apologize for the recent incident, and work hard to get the Pakistani military and ISI on board with a political deal to end the war. Everyone who’s worked on Afghanistan knows roughly what such a deal would look like, although there are many obstacles between here and there. Unfortunately for the White House, the obstacles are piling up, not getting removed.