A Pakistani protester holds a burning U.S. flag during a Jan. 11 demonstration against drone attacks in Pakistani tribal areas. As relations between the two countries nations sink, officials try to figure out a way forward. (S.S. Mirza/AFP/Getty Images)

In a call to her Pakistani counterpart this month, Secretary of State Hillary Rodham Clinton reiterated the Obama administration’s counterterrorism “red line”: The United States reserved the right to attack anyone who it determined posed a direct threat to U.S. national security, anywhere in the world.

Foreign Minister Hina Rabbani Khar responded in kind, telling Clinton that Pakistan’s red line was the violation of its sovereignty. Any unauthorized flight into its airspace, Khar bluntly told Clinton, risked being shot down.

The conversation, recounted by U.S. officials, was one of the few high-level exchanges between the two governments in recent months, and it illustrated the depths to which U.S.-Pakistan relations have fallen after an inadvertent November border clash in which a U.S. air assault killed 24 Pakistani soldiers.

Since then, Pakistan’s border crossings have remained closed to U.S. and NATO supplies in transit to the Afghan war. At Pakistan’s demand, U.S. personnel have evacuated a secret drone airstrip, and the number of American military trainers in the country has been cut to a fraction of previous levels.

Marc Grossman, the administration’s top diplomat in charge of Afghanistan and Pakistan, asked to visit Islamabad during a current trip to the region, but Pakistani officials responded that it was not convenient.

The “fundamentals” of mutual interest in destroying al-Qaeda and safely managing Pakistan’s nuclear arsenal haven’t changed, said a senior Obama administration official, who, like several sources in this article, discussed sensitive diplomatic matters on the condition of anonymity. But the two countries are groping their way toward what he called “a new normal” — somewhere between the strategic alliance that President Obama once proffered in exchange for Pakistan severing its ties with militants, and a more businesslike arrangement with few illusions.

“It’ll be much more realpolitik,” another U.S. official said. “It’s getting away from the grandiose vision of what could be to focusing on what is.”

A senior Pakistani military official said, “We’ve had some glorious times,” citing past interludes of intelligence and military cooperation in pursuit of Pakistan-based al-Qaeda and Taliban militants.

But the military official also spoke emotionally about the deaths of the 24 soldiers in November and said the incident would not soon be forgotten. The same was true of what he said were other insults in 2011, including the shooting deaths of two Pakistanis by a CIA contractor in Lahore, the U.S. Special Operations raid that killed Osama bin Laden in a Pakistani suburb and the assertion by Adm. Mike Mullen, then chairman of the Joint Chiefs of Staff, that the insurgent Haqqani network was a “veritable arm” of Pakistani intelligence.

Pakistan, the military official said, wants some “significant changes” in the way the two countries do business.

After the November border clash, the Obama administration suspended its regular drone attacks inside Pakistan to avoid further unsettling relations, U.S. officials said. And in a rare display of deference early this month, the CIA informed the Pakistani government that it planned a drone strike against a terrorist target in the North Waziristan tribal region and asked Islamabad’s permission. When Pakistan declined, the strike was canceled, officials said.

But on Jan. 10, barely a week later, the 55-day drone hiatus ended abruptly with a strike that killed four alleged militants in North Waziristan, followed by another strike two days afterward. Although officials said Pakistan was notified in advance, permission was not sought.

Reviewing cooperation

A Pakistani parliamentary committee, with input from feuding military and civilian political factions, is conducting what Prime Minister Yousuf Raza Gilani on Saturday called “a full review of the terms of cooperation” with the United States and the U.S.-led international coalition in Afghanistan.

“Pakistan’s sovereignty and territorial integrity are not negotiable,” Gilani said.

A senior Pakistani government official said the committee’s recommendations will probably include a demand for explicit U.S. assurances that there will be no violation of sovereignty — no American boots on the ground, no more unilateral raids, no manned airstrikes. The official said there is likely to be some arrangement on drone attacks, with Pakistan calling for large reductions in their number and geographic scope, and demanding prior notification and approval of every strike.

Any explicit agreement on drones would be a major change from past practice, in which Pakistan has privately agreed to strikes but publicly denounced them.

Pakistan also wants more explicit compensation for U.S. and NATO supplies transiting its ports and roads, perhaps in the form of taxes. And it wants more comprehensive information about CIA operations and personnel. “There are over 1,000 houses in Pakistan that have been hired by the U.S. Embassy, and we don’t know who lives in them,” the Pakistani official said.

Yet in a recent parliamentary briefing, Finance Minister Abdul Hafiz Sheikh cautioned against a complete breakdown of U.S. ties, saying the nation’s economy could not absorb the shock, according to a second Pakistani official.

In addition to receiving nearly $3 billion in annual military and civilian assistance — much of which has been withheld by the Obama administration over the past year of conflict — Pakistan is well aware of the U.S. influence in international financial institutions and other important world forums.

U.S. peace talks with the Taliban are also a top issue for Pakistan, which has provided sanctuary for the Haqqani network, a Taliban ally, as well as the main Taliban leadership as leverage to protect its long-term interests in Afghanistan. Although the Obama administration and the Afghan government have offered the Pakistanis a role in the peace talks, both mistrust their motives.

Role in the Afghan war

In the United States, Obama is under political pressure to show Islamabad who is the global boss. Patience here has grown paper-thin with what is seen as Pakistani double-dealing and intransigence that is getting in the way of efforts to wind down the Afghan war.

An emerging U.S. military narrative, in preparation for internal administration discussions over the pace of troop withdrawal, holds that the U.S.-led coalition cannot quickly consolidate its considerable gains in Afghanistan because of Pakistan. A heavy U.S. footprint needs to be maintained, a senior Pentagon official said, because Pakistan refuses to crack down on the Haqqani network, whose forces regularly attack coalition troops in Afghan border provinces.

Pakistan also has snubbed U.S. efforts to boost the Afghan economy with a gas pipeline that would run from Turkmenistan through Afghanistan to Pakistani ports. Instead, it has reiterated its plans to proceed with an alternative pipeline from Iran.

Obama administration officials said they will resist responding until Pakistan’s Parliament has finished its review of relations with the United States. “We have views on where we’d like to see this go,” a U.S. official said. But it will “take another week or two . . . for their internal process to come to some kind of formal communication that would be communicated back to us.”

U.S. officials question whether Pakistan has the ability or the desire to shoot down U.S. aircraft, whether armed drones; unarmed, unmanned planes that regularly conduct surveillance over border areas; or manned attack and military transport planes that sometimes stray unintentionally over the border.

They said there have been at least two accidental violations of Pakistani airspace in recent weeks by piloted aircraft in Afghanistan, but both incidents were calmly defused by border coordination centers on the Afghan side.

Brulliard reported from Islamabad. Staff writers Greg Miller and Greg Jaffe, and special correspondent Shaiq Hussain in Islamabad, contributed to this report.