The firestorm in Pakistan-US relations set off by the November 26 NATO assault on Pakistan’s border posts was a crisis waiting to happen.

It was in large part the result of an increasingly aggressive and unilateral strategy applied to the region by the Obama administration. This has given US troops on the ground a freer rein to carry out kinetic operations with scant regard for the Afghan-Pakistan border and for Pakistan’s sovereignty.

This wasn’t after all the first cross-border violation. But it was the most serious and seemed to mark a fateful turn in an already fractured relationship. With 24 Pakistani soldiers left dead this was a breach too far. It triggered a wave of public fury and protest demonstrations that have yet to subside.

Washington grudgingly offered ‘regret’ over the loss of lives but no apology. It took President Obama eight days to personally convey his condolences. The delay made the call seem more transactional than heart-felt. This bid to address inflamed ties appeared to be too little and too late to calm public opinion.

The refusal by the Obama administration to take responsibility for a tragic incident fuelled unprecedented official and public anger. Worse, contradictory accounts of the incident leaked to the media by US military officials seemed designed to shift the responsibility for the tragedy to Pakistani troops. This was in utter disregard of the reality that 24 soldiers were left dead on one side of the border with no casualties on the other side.

The imperious tone of officials quoted in these news stories, along with their why-should-we-apologise refrain, aggravated the situation and strengthened the argument of those who questioned Islamabad’s alliance with America. If Washington couldn’t even bring itself around to saying sorry and express genuine empathy, assertions by its officials of wanting to maintain ties with Pakistan on the basis of ‘mutual respect’ carried little weight.

For Pakistan this was one transgression too many. Several red lines had been crossed. Islamabad retaliated by closing down the Nato supply route, demanding that Shamsi airbase be vacated and vowing to review its relationship with America. It also announced it would not attend the conference on Afghanistan in Bonn. The argument that Pakistan was isolating itself from international efforts to shape Afghanistan’s future overlooked a fundamental fact – that on-ground realities would dictate that future, not well-attended conferences.

Even after the swift and robust position taken by Pakistan, Washington appeared to underestimate Islamabad’s resolve to stay the course. Some US officials expected that the belated expression of condolences, minus an apology, would be sufficient for Pakistan to resume business as usual.

They failed to understand that Pakistan’s response – a national response despite civil-military mistrust and government-opposition tensions – marked a loss of patience with the high-handed way in which the US continued to treat Pakistan. It also reflected the accumulation of grievances from the previous three crises and other fraught encounters this year. The January showdown over the murder of two Pakistanis by a CIA contractor, the US stealth mission in May to kill Osama bin Laden on Pakistani soil and Admiral Mullen’s inflammatory remarks in September left a lasting impression on Islamabad.

In different ways these episodes demonstrated a disregard for Pakistan’s sensitivities and concerns but above all its sovereignty. Diplomatic patch up efforts that followed every crisis did little to reassure Pakistan that Washington was willing to change its coercive approach.

Most significantly Pakistan saw little if any US responsiveness to the core demands it made after May 2. They included: a) Renunciation by the US of any unilateral option; b) Vacation of Shamsi; c) Resolution of the Drones issue and d) Transparency and reciprocity in intelligence cooperation. What also poisoned relations was the tone of the conversation Washington chose to have with Islamabad, often lacing it with ultimatums and threats of aid-cut offs. Gratuitous public comments and accusations by US officials that further whipped up anti-Pakistan sentiment in America came to be seen as deliberate efforts to pressure-by-leaks and demonisation. All this began to shrink the government’s political space to sustain the usual cooperation with the US.

Islamabad’s post-May effort to ‘reset’ ties with Washington stumbled in the face of tensions unleashed by unrelenting crises. Seen from this perspective Pakistan’s response after November 26 represented an effort to redefine the terms of its cooperation. It was not a knee-jerk reaction out of pique that some in Washington seemed to mistakenly construe. And by not sending a delegation to Bonn, the message to Nato countries was that unless they decided whether to treat Pakistan as a target or a partner, Islamabad was no longer prepared to be both. Nor, as Prime Minister Gilani put it, would Pakistan serve as a scapegoat for Nato’s failure to secure a military victory in Afghanistan.

The ongoing crisis has also laid bare the lack of clarity or consensus within the Obama administration over conducting policy towards Pakistan. In the immediate aftermath of the November 26 attack, many State Department officials advocated some form of apology to defuse the situation but the Pentagon and its allies in the intelligence community would have none of that. Instead they used shifting accounts of the incident to pre-empt any such move.

Characteristically the White House dithered and procrastinated. Fearing that an apology would be ‘politically costly’ in an election year, it deferred for all practical purposes to the military’s act-tough-with- Pakistan view. This meant, according to a perceptive American commentator, that commanders on the ground called the shots on Pakistan policy.

This reinforced a familiar aspect of President Obama’s decision making on national security issues including Afghanistan where he has been inclined to frequently cede policy to the Pentagon. This also explains some of the recent turbulence in ties with Pakistan. And it points to a fatal flaw in his regional approach, which views Pakistan mostly through the prism of the Afghan war.

Where does all this leave ties between the two countries? The relationship is in a state of near-breakdown at a pivotal moment for the region. As 2014 approaches – when Nato’s combat forces will pull out of Afghanistan – the US military seems more interested in stepping up the fighting than winding down the war to support diplomatic efforts for a negotiated settlement. A political solution is President Obama’s stated goal. An orderly transition rests on securing this objective. But his military commanders’ preference to fight on till 2014 is at odds with the pressing goal to start serious talks with the Taliban.

At the heart of the present disagreement with Pakistan and the source of much of the recent strains is this: Pakistan believes military de-escalation is necessary for the political strategy to work, but Washington’s strategy, still defined by the Pentagon, is to fight-and-talk. This is translating into no-holds-barred kinetic operations by US-led Nato forces including dreaded night raids in Afghanistan and other frenetic actions to gain military supremacy that has proved elusive so far.

The irony in all of this is that Pakistan and the US appear to want the same outcome in Afghanistan and the region – a political settlement that allows western forces a safe exit and enables Afghanistan to move towards peace and stability. The two countries also want to establish a regional environment that prevents the return or regeneration of Al-Qaeda.

These objectives have all but been obscured by a combination of western actions aimed at avoiding the impression of defeat in Afghanistan, contradictions and confusion in US policy and divergences over strategy between Washington and Islamabad. There are compelling reasons for both countries to avoid a rupture in relations. But by its latest moves Islamabad has signalled that future cooperation will have to rest on mutual accommodation of each other’s security concerns and not imposition of one side’s needs with no regard for Pakistan’s sovereignty and interests.

Dr. Maleeha Lodhi is a former Pakistani Ambassador to the United States and special adviser to the Jang Group/GEO. This article originally appeared in The News International.