The unilateral U.S. raid that killed Osama bin Laden created a spike in mutual recriminations between U.S. and Pakistani politicians, but their fundamental conflict of interest over Afghanistan was already driving the two countries toward serious confrontation.
The pivotal event in relations between the Obama administration and Pakistan was the decision by President Barack Obama to escalate the war in Afghanistan in 2009, despite the knowledge that Pakistan was committed to supporting the Taliban insurgents as a strategic policy in its conflict with India.
Obama launched a desperate, last-minute effort to get some kind of commitment from the Pakistanis to reduce their support for the Taliban before the decision to escalate the war. But he did not reconsider the decision after that effort had clearly failed.
It was always understood within the Obama administration that any public recognition that Pakistan was committed to supporting the Taliban could be politically dangerous to the war effort.
As a result, Obama's national security team decided early on to deny the complicity of Pakistani Chief of Staff Ashfaq Parvez Kayani and director of the ISI intelligence agency Shuja Pasha, despite the knowledge that they were fully behind the policy.
On March 26, 2009, a story in the New York Times provided the most detailed news media account up to that date of Pakistani assistance to the Taliban. But the story quoted anonymous U.S. officials as blaming "mid-level ISI operatives" and expressing doubt that top Pakistani officials in Islamabad were directly coordinating the clandestine efforts by ISI operatives to assist the Taliban.
That did not reflect the briefing Obama had gotten from George W. Bush's director of national intelligence, Mike McConnell, after his election. McConnell had learned from communications intercepts that Kayani considered the Haqqani network, which was being targeted as the most serious threat to U.S. troops n Afghanistan, as a "strategic asset."
As Obama approached a decision on Gen. Stanley A. McChrystal's request for another troop increase of as much as 40,000 troops, the Pakistani military's determination to use the Taliban and the Haqqani network to advance Pakistani interests in Afghanistan was a major issue in the policy debate.
Opponents of the troop surge request, including Vice President Joe Biden, deputy national security adviser Tom Donilon and Afghanistan War coordinator Douglas Lute, argued that the Pakistanis were not going to change their policy toward Afghanistan, according to Bob Woodward's account in Obama's Wars.
Biden argued in a meeting on Sept. 13, 2009, that Pakistan was determined to avoid an Afghan government "led by a Pashtun sympathetic to India" -- i.e., Afghan President Hamid Karzai. The conclusion was that the Pakistanis would continue to aid the insurgency the U.S. was trying to defeat. Despite that argument, as the policy-making process was entering its final weeks, Obama tried to exert high-level pressure on Pakistan.
In a Nov. 11, 2009, letter to Pakistani President Asif Ali Zardari, Obama said Pakistan's use of such "proxy groups" as Haqqani and the Taliban would no longer be tolerated, as Woodward recounts. National Security Adviser James Jones and Counterterrorism adviser John Brennan were sent to Islamabad to deliver the message.
Obama wanted Pakistan to understand that he would take unilateral action against the Taliban and Haqqani safe havens in Pakistan, including accelerated drone strikes and commando raids, unless Pakistani forces attacked them.
That message was clearly received. A Pakistani official told the New York Times, "Jones' message was if that Pakistani help wasn't forthcoming, the United States would have to do it themselves."
The week of Nov. 17, 2009, CIA Director Leon Panetta met with Pasha and other top Pakistani officials, and complained about the presence of the Taliban leadership headquarters in Quetta, Baluchistan, according to Woodward's account. Panetta cited intelligence that bombs were being made there, then "taken across the border and blowing up Americans."
Panetta proposed joint U.S.-Pakistani operations on the ground aimed at the Quetta Shura, but Kayani refused. In a response to Obama's letter late in November, Zardari voiced the Pakistani military's rationale for Pakistan's use of Afghan insurgents to protect its interests in Pakistan. He charged that "neighboring intelligence agencies" -- meaning India -- "are using Afghan soil to perpetuate violence in Pakistan."
And Zardari did not give a clear response to Obama's invitation to plan joint operations against those forces.