Within the country, friction between the military and civilian leaders had been intensifying since the Bin Laden killing. In October, military leaders seized on an unsigned memo written after the Bin Laden raid that asked the United States for help averting a coup and charged that it was the work of an ally of President Asif Ali Zardari.

The normally soft-spoken prime minister, Yusuf Raza Gilani, lashed out at the Army as a “state within a state’’ in December 2011 and in January 2012 challenged the military directly by firing his defense secretary, a retired general and confidant of Pakistan’s army chief.

On Jan. 13, the country’s lawmakers framed a resolution designed to bolster the nation’s civilian leadership at a time of sharpening tension with the powerful military. The resolution pledging “full confidence and trust” in the political leadership is to be put to a vote in Parliament on Jan. 16. After the resolution was introduced, Mr. Gilani declared: “Either there will be a democracy or dictatorship.”

Clash Between Military and Civilian Leaders

Pakistan’s Supreme Court escalated its clash with the government on Jan. 16 by initiating contempt of court proceedings against Mr. Gilani for failing to pursue corruption charges against his boss, Mr. Zardari. 

The court was clearly infuriated after the government’s lawyer said that the government had given no instructions on how to respond to the court’s demands.

Justice Nasir ul Mulk ordered Mr. Gilani to appear Jan. 19 to explain why he should not be charged with contempt, a charge that could open to the door to his dismissal from office. Hours later, Prime Minister Gilani promised to obey the judicial order.

Prime ministers are rarely called to court in Pakistan and the order was a measure of the seriousness of the clash between the two institutions, as a hawkish military hovers in the background amid sporadic rumors of a coup.

The week before, the military, which has done little to disguise its loathing for the president and prime minister, warned of “potentially grievous consequences” if the government did not halt its unusually frank public criticism of the army.

Few analysts believe a coup is imminent, but speculation is rife that the military is using the court as a means of ousting President Zardari through constitutional means.

The Haqqani Memo

The rising tensions between civilians and the military boiled over in October 2011 with the release of an unsigned memorandum purportedly asking the Obama administration’s help to curb the military’s influence and avert a possible coup. Husain Haqqani, a close aide to Mr. Zardari, was forced to resign as Pakistan’s ambassador in Washington on Nov. 22 after accusations that he had orchestrated the memo, a charge he denies.

In December, when Mr. Zardari was in Dubai seeking medical treatment, the military pushed the Pakistani Supreme Court into investigating whether Mr. Zardari’s government was behind the memo.

The case brought tensions between Pakistan’s military and its civilian leaders to perhaps its highest pitch since Mr. Zardari was elected. An extraordinary outburst from the normally soft-spoken prime minister, Yusuf Raza Gilani, warning of a possible coup, led to an unusual pledge by the military’s leader, Gen. Ashfaq Parvez Kayani, saying that the army supported democracy.

However, General Kayani stressed that “there can be no compromise on national security,” alluding to the differences with the civilian government over investigations into the contentious memo.

The civilian government denied having anything to do with the memo and warned that Parliament, the media, the civil society and the international community would not tolerate a military dictatorship in Pakistan. But in a filing to the Supreme Court, Gen. Ashfaq Parvez Kayani, the Pakistani Army chief, asked the court to investigate the controversial memo and its origins fully, saying it “unsuccessfully attempted to lower the morale of the Pakistan Army.”

On Dec. 30, the Supreme Court ordered an investigation into the memo, dealing a blow to the country’s civilian leaders.

Then in January 2012, Mr. Gilani fired the secretary of defense, Naeem Khalid Lodhi, a former corps commander, accusing him of “gross misconduct and illegal action” and of “creating misunderstanding between the state institutions.” He replaced the former general with a civilian aide, Nargis Sethi.

The defense secretary is ordinarily appointed with the consent of the army chief and acts as a bridge between the civilian government and military. The role is more powerful than that of defense minister, a position that is filled by a politician from the governing party.

Military officials warned that the army would be likely to refuse to work with the newly appointed defense secretary, signaling the possibility of a serious rupture between the army and the civilian government. “

A Lull in Drone Strikes; Insurgents Regroup

Insurgents have increasingly been taking advantage of tensions between the two countries. In January 2012, an article in The New York Times reported that the Central Intelligence Agency, hoping to avoid making matters worse while Pakistan completed a review of its security relationship with the United States, had not conducted a drone strike in Pakistan in nearly two months.

The lull in American drone strikes has helped embolden Al Qaeda and several Pakistani militant factions to regroup; increase attacks against Pakistani security forces and threaten intensified strikes against allied forces in Afghanistan, American and Pakistani officials said.

According to diplomats and intelligence analysts, the pause in C.I.A. missile strikes has offered greater freedom of movement to an insurgency that was splintered by in-fighting and battered by American drone attacks. Several feuding factions said that they were patching up their differences, at least temporarily, to improve their image after a series of kidnappings and, by some accounts, to focus on fighting Americans in Afghanistan.

Pakistan ordered drone operations at its Shamsi air base closed after the airstrike on Nov. 26, but C.I.A. drones flying from bases in Afghanistan continue to fly surveillance missions over the tribal areas. The drones would be cleared to fire on a senior militant leader if there was credible intelligence and minimal risk to civilians, American officials said. But for now, the Predator and Reaper drones are holding their fire, the longest pause in Pakistan since July 2008.

The Pakistani groups include the Pakistani Taliban, an umbrella group led by Hakimullah Mehsud that has mounted attacks against the Pakistani state since the group was formed in 2007. They also include the Haqqani network and factions led by Maulvi Nazir of South Waziristan and Hafiz Gul Bahadur of North Waziristan, which already target NATO soldiers and have tacit peace agreements with the Pakistani military.

Drone strikes resumed in mid-January.

Executions by Taliban Insurgents

In early January 2012, Taliban insurgents executed 15 kidnapped Pakistani soldiers and dumped their bodies on a hilltop in northwestern Pakistan, government and military officials said, in retaliation for the killing of a militant commander by government forces.

The soldiers were kidnapped on Dec. 23, 2011, after dozens of Taliban insurgents overran a fort in the Mullazai area in the Tank district of South Waziristan, one of the restive tribal regions straddling the border with Afghanistan. Officials said efforts had been made to secure their release.

The executions followed the death of a high-ranking Taliban commander on Jan. 1 and came just days after local media reported that several factions of the Taliban had formed a united front and had vowed not to attack the Pakistani military.

The soldiers were members of the Frontier Constabulary, which is run by Pakistani police authorities. It has about 70,000 paramilitary soldiers who man checkpoints in Khyber-Pakhtunkhwa Province and provide security at foreign embassies and consulates in major cities across Pakistan.

Sunni Extremist Group Linked to Bombings

An explosion ripped through a crowd of Shiite Muslims in central Pakistan in mid-January 2012, killing at least 17 people in one of the largest such attacks in recent times in Pakistan’s most populous province.

The police said a bomb in Khanpur, a town in the southern part of Punjab, killed Shiite worshipers as they streamed out of a mosque after a religious ceremony commemorating the 40th day after the death anniversary of the Prophet Muhammad’s grandson Imam Hussein, a highly revered figure in Shiite Islam.

Sunni extremist groups, who view Shiites as heretics, have been implicated in a rising number of a sectarian attacks, according to human rights monitors.

Lashkar-e-Jhangvi, a militant group with historical ties to the Pakistani security establishment, claimed responsibility for the attack. In early December 2011, the group also took responsibility for an attack in the Afghan capital, Kabul, that killed at least 63 Shiite worshipers.

Overview

Pakistan was born as an explicitly Muslim state, and the wrestling between its secular and Islamic natures has never been so pronounced as in recent years. Its other sources of unrest, including the military’s role as the arbiter of power — there have been four coups in its 60 years of independence — its rampant corruption and political instability, have been joined by the rise of Islamic militant groups that control of parts of the country’s western half and have launched attacks in the heart of its largest cities.

After the attacks of Sept. 11, 2001, Pakistan entered into an alliance with the United States that it later claimed was the result of coercion. In 2002, it came to the brink of war with India after Islamic members of a Pakistani militant group attacked India’s Parliament.

The following years were tumultuous even by Pakistan’s standards, as its military ruler, Gen. Pervez Musharraf, was forced from office and a combination of the Taliban and home-grown Islamic militants spread their control from country’s mountainous western border ever further toward the capital.

General Musharraf’s successor was Asif Ali Zardari, who inherited control of the Pakistan Peoples Party from his wife, Benazir Bhutto, after she was gunned down at a political rally in 2008. But Mr. Zardari has proved to be a weak and unpopular president, whose main achievement seems to be juggling members of the Supreme Court to keep old corruption charges against him at bay.

Even that seemed to have failed in January 2012, when the Supreme Court threatened to dismiss Prime Minister Yousaf Raza Gilani for failing to comply with court orders to reopen corruption cases against Mr. Zardari.

Power has continued to be exercised largely by the military — if more discreetly — and its leader, Gen. Ashfaq Parvez Kaylani, is widely regarded as the country’s most powerful figure. And while General Kaylani has pursued a more aggressive approach toward battling the militants, launching offensives to reclaim control of the western provinces, American officials remain convinced that portions of the military are still supporting the Taliban in Afghanistan.

The summer of 2010 produced Pakistan’s worst flooding in 80 years (more on Pakistan’s 2010 floods here). The government’s poor performance in the aftermath of the floods, which left 20 million people homeless and the nation dependent on handouts from skeptical foreign donors, laid bare the deep underlying tensions between military and civilian leaders as the military pushed for a shake-up of  elected officials in response to popular anger.

With the death of Osama Bin Laden in May 2011, perhaps the central reason for an alliance with the U.S. forged on the ashes of 9/11 has been removed, at a moment when relations between the countries are already at one of their lowest points as their strategic interests diverge over the shape of a postwar Afghanistan.

2007: Musharraf Era Ends

In 2007, Pakistan’s military ruler, Gen. Pervez Musharraf, was forced from power. He was replaced by neither of his longtime rivals, Nawaz Sharif or Benazir Bhutto, who was killed by a bomb at a campaign rally. A tide of strong emotion swept Bhutto’s party into power in parliamentary elections in 2008, and her widower, Asif Ali Zardari, became president.

General Musharraf’s tenure was dominated by the aftermath of the Sept. 11th attacks, by political instability and the rise of Islamic extremist groups.

After 9/11, the United States demanded that Pakistan turn against the Taliban and al Qaeda. Mr. Musharraf agreed but then walked a tightrope between satisfying the Bush administration without inflaming Islamic groups that strongly support al Qaeda. The mountains of western Pakistan became a haven for Al Qaeda and the Taliban and a launching pad for increasing numbers of extremist attacks in Afghanistan and within Pakistan.

Mr. Musharraf’s downfall began with his attempt to force out the chief justice of Pakistan’s Supreme Court, Iftikhar Mohammed Chaudhry, in the spring of 2007, which was widely protested. Mr. Musharraf was forced to backtrack. Under pressure from the Bush administration, he began negotiations with Ms. Bhutto, a former prime minister then in exile, about a power sharing agreement.

No agreement was reached, and Mr. Musharraf declared a state of emergency. Hundreds of political opponents were arrested and a majority of the Supreme Court was forced to resign. On Nov. 28, 2007, Mr. Musharraf gave up his military rank, and two weeks later ended emergency rule. By that time, Ms. Bhutto and Nawaz Sharif, the prime minister Mr. Musharraf had deposed, were vigorously campaigning against Mr. Musharraf.

2008: The Zardari Presidency

On Dec. 27, 2007, Benazir Bhutto was killed by a bomb detonated as she left a large rally, throwing the country into deep mourning. A parliamentary election was postponed until February 2008, when Mr. Musharraf’s party was routed as Mr. Zardari took charge of her political apparatus. Mr. Zardari and Mr. Sharif formed a governing coalition, which declared that it would seek the impeachment of Mr. Musharraf, who soon after announced his resignation.

In September 2008, Mr. Zardari was elected president, completing a remarkable swing from prisoner to exile to marginal political player to the country’s central figure.

In November 2008, tensions with India returned to the forefront after the terrorist attacks in Mumbai, which were quickly linked to a Pakistani militant group, Lakshar e-Taiba. The country soon faced a financial crisis as well, as the global financial crisis cut Pakistan off from credit it desperately needed. The government reached agreement with the International Monetary Fund for a $7 billion loan.

In February 2009, Mr. Zardari tried to force Mr. Sharif out of office, but relented in the face of huge protests and Mr. Sharif emerged as the most popular politician in the country. Mr. Zardari has seen his popularity ratings plummet, largely because of concerns about Pakistan’s faltering economy and a general sense that the country is headed in the wrong direction.

In January 2011 his government survived another crisis only by promising to resume fuel subsidies and put off efforts to expand tax collection, two steps that the United States and international lenders considered crucial to maintaining the country’s solvency.

For the time being, Pakistan may remain dependent on international assistance, including billions of dollars in military and civilian aid from the United States, even as fewer than 2 percent of Pakistanis pay income tax, with many wealthy members of government among those who pay nothing. The country’s tax revenues will remain among the lowest in the world.

Musharraf in Exile; Charged in Bhutto Case

In 2008 Mr. Musharraf fled the country under threat of impeachment and has been living in exile in London and Dubai. He was charged in February 2011 in the Bhutto case, though Pakistani officials did not provide details of their accusations against him. In August 2011 a Pakistani court ordered that Mr. Musharraf’s property be seized and his bank accounts frozen for failing to respond to subpoenas.

2009: Domestic Campaign Against the Taliban

Pakistanis long supported the Taliban and other militant groups as allies to exert influence in neighboring Afghanistan and as a hedge against India. Unlike Afghans, they never lived under Taliban rule, and were slow to absorb its dangers.

Through 2008 and early 2009 the influence of the Taliban spread from the remote mountains along the Afghanistan border. The region of Swat, formerly a lure for tourists not far from the capital, became the scene of infiltration, intimidation and constant fighting, and in early 2009 the government reached a truce agreement with militants there. Mr. Zardari signed a measure that would impose Islamic law in the valley. 

Soon afterward the Taliban took over Buner, an adjoining district only 60 miles from Islamabad. The conquest shook the central government, as well as the middle and upper classes across the country. It also caused American officials to apply enormous pressure on Pakistan to act.

The ensuing military campaign, begun in May 2009, seemed to be prosecuted with a new resolve, in what appeared to be a change of heart in the Pakistani Army, which had supported the militants for many years. Unaccustomed to urban guerrilla warfare, the military first concentrated on fighting in the rural and mountainous areas of Swat. The ensuing exodus of 1.3 million refugees was the largest mass migration of Pakistanis since the country was partitioned from India more than 60 years ago.

As the battle in Swat died down, the army’s mission turned to the rugged Taliban stronghold of South Waziristan, home to Baitullah Mehsud, Pakistan’s enemy No. 1. Mr. Mehsud was killed in August 2009 in a United States drone strike, but thousands of fighters remained entrenched in mountain terrain that is nearly impossible for conventional armies to navigate.

Many of the Pakistani Taliban fighters organize and rest in North Waziristan under the protection of Sirajuddin Haqqani, the Afghan Taliban leader who runs a network of several thousand fighters of his own. Allied with the Taliban and backed by Al Qaeda, the Haqqani group makes up a significant part of the insurgency in Afghanistan, too, and American officials have pressed the Pakistani Army for an offensive against them. But the brunt of the effort against Al Qaeda and the Haqqani fighters is borne by American drone strikes launched with Pakistan’s acquiescence.

Suspicions about the role of the Pakistani military in the rise of the Taliban were underscored by the release in July 2010 of a trove of thousands of classified American military documents. The documents, made available by WikiLeaks, suggest that Pakistan, an ostensible ally of the United States, allows representatives of its spy service to meet directly with the Taliban in secret strategy sessions to organize networks of militant groups that fight against American soldiers in Afghanistan, and even hatch plots to assassinate Afghan leaders.

2010: Flooding Devastates the Nation

The summer of 2010 produced Pakistan’s worst flooding in 80 years (more on Pakistan’s 2010 floods here). In a televised address on Aug. 14, Prime Minister Yusuf Raza Gilani said 20 million people, about one-ninth of the population, had been displaced by the disaster. Millions were without food, shelter and clean water.

Flooding began on July 22 in the province of Baluchistan, and the swollen waterways poured across the Khyber-Pakhtunkhwa Province in the northwest before flowing south into Punjab and Sindh. Even as Pakistani and international relief officials scrambled to save people and property, they despaired that the nation’s worst natural calamity had ruined just about every physical strand that knit this country together — roads, bridges, schools, health clinics, electricity and communications.

The devastation raised fears of further instability. Hard-line Islamic groups stepped in to provide aid where the government failed to reach; the United States also sent aid with an eye to improving its reputation among ordinary Pakistanis.

The Pakistani military, angered by the inept handling of the floods and alarmed by a collapse of the economy, pushed for a shake-up of the elected government, and in the longer term, even the removal of President Zardari and his top lieutenants. However, the military’s preoccupation with its war against militants and reluctance to assume responsibility for the economy directly led it to emphasize it is not eager to take over the government.

Drone Warfare Escalates

An escalation of attacks in Pakistan announced by the Obama administration in late 2010 largely involved increased drone strikes. The move reflected mounting frustration both in Afghanistan and the United States that Pakistan has not been aggressive enough in dislodging militants in the mountains. More than 1,900 insurgents in Pakistan’s tribal areas have been killed by American drones since 2006, according to the Web site longwarjournal.com. And one of Pakistan’s most wanted militants, Ilyas Kashmiri, was reported dead in a June 2011 C.I.A. drone strike.

The number of civilian deaths caused by drone strikes has become a hotly contested issue between Pakistan and the United States. In June 2011, Obama administration officials said the C.I.A.’s drone program in Pakistan had killed about 600 militants and no civilians since May 2010. However, a new report from the British Bureau of Investigative Journalism, a Web-based reporting project, concluded that at least 45 civilians were killed in 10 strikes during the last year.

2011: Bin Laden Killing Raises Tensions

The death of Osama Bin Laden and the circumstances that allowed him to reside quietly in a three-story house on the edge of the Pakistani town of Abbottabad, which houses military garrisons, have sharply increased tensions between the American and Pakistani governments.

For nearly a decade, the United States paid Pakistan more than $1 billion a year for counterterrorism operations whose chief aim was the killing or capture of Bin Laden, who slipped across the border from Afghanistan after the American invasion.

The circumstance of Bin Laden’s death may not only jeopardize that aid, but will also no doubt deepen suspicions that Pakistan has played a double game, and perhaps even knowingly harbored the Qaeda leader. Some in Washington see the detention of C.I.A. informants after the raid as illustrative of the disconnect between Pakistani and American priorities at a time when they are supposed to be allies.

Even before the strike against Bin Laden, Pakistan had demanded in April 2011 that the United States scale back its number of C.I.A. operatives and Special Operations forces working in the country, and suspend drone strikes on militants in northwest Pakistan. The reductions were personally demanded by the chief of the Pakistan army, Gen. Ashfaq Parvez Kayani.

The reputation of the army, the most powerful and privileged force in the country, was severely undermined by the American raid.

That American helicopters could fly into Pakistan, carrying a team to kill the world’s most wanted terrorist and then fly out undetected has produced a stunned silence from the military and its intelligence service that some interpret as embarrassment, even humiliation.

In July 2011, the Obama administration suspended and, in some cases, canceled hundreds of millions of dollars of aid to the Pakistani military, in a move to chasten the country for expelling American military trainers and to press its army to fight militants more effectively. Coupled with a statement from the top American military officer linking Pakistan’s military spy agency to the recent murder of a Pakistani journalist, the halting or withdrawal of military equipment and other aid to Pakistan illustrates the depth of the debate inside the Obama administration over how to change the behavior of one of its key counterterrorism partners.

In the fall, the administration stepped up its efforts at brokering a deal with militants before the last of 33,000 American “surge” troops prepare to pull out of Afghanistan by September. 

But even inside the administration, the new initiative was met with deep skepticism, in part because the Pakistani government has developed its own strategy, one at odds with Mrs. Clinton’s on several key points. One senior American official summarized the Pakistani position as “Cease-fire, Talk, Wait for the Americans to Leave.”

In short, the United States is in the position of having to rely heavily on the ISI to help broker a deal with the same group of militants that leaders in Washington say the spy agency is financing and supporting.

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