Is the Kashmir American Council’s Fai’s Arrest a Reflection of Tense Relations Between ISI & CIA?

According to NYT, ISI spent $4 million over two decades in a covert attempt to tilt American policy against India’s control of much of Kashmir — including funneling campaign donations to members of Congress and presidential candidates, the F.B.I. claimed in court papers unsealed on July 19, 2011.

The allegations of a long-running plan to influence American elections and foreign policy come at a time of deep tensions between the United States and Pakistan — and in particular ISI— amid the fallout over the American raid that killed Osama bin Laden at a compound in Abbottabad on May 2.

The FBI made the allegations in a 43-page affidavit filed in connection with the indictment of two United States citizens on charges that they failed to register with the Justice Department as agents of Pakistan, as required by law.

One of the men, Zaheer Ahmad, is in Pakistan who is also the chief executive of Shifa International Hospital. The other, Syed Fai, lives in Virginia and was arrested on July 19.

Mr Fai is the director of the Kashmiri American Council, a Washington-based group that lobbies for and holds conferences and media events to promote the cause of self-determination for Kashmir.

The timing of the crackdown is intriguing. Both the individuals are American citizens and Fai has been living in the United States for decades. Why have the American authorities suddenly discovered the clandestine activities of these individuals; is this a tit for tat for mistreating Raymond Davis who was a CIA agent. It appears that ISI is fast losing its clout with the CIA and the relations between the two agencies are tense.

According to the affidavit, the activities by the group, also called theKashmiriCenter, are largely financed by the ISI, along with as much as $100,000 a year in related donations to political campaigns in theUnited States.

Foreign governments are prohibited from making donations to American political candidates.

“Mr. Fai is accused of a decades-long scheme with one purpose — to hide Pakistan’s involvement behind his efforts to influence the U.S. government’s position on Kashmir,” Neil MacBride, the United States Attorney in the Eastern District of Virginia, said. “His handlers inPakistanfunneled millions through the Kashmir Center to contribute toU.S.elected officials, fund high-profile conferences and pay for other efforts that promoted the Kashmiri cause to decision-makers inWashington.”

A spokesman for the Pakistani Embassy denied any connection to matter, saying, “Mr. Fai is not a Pakistani citizen, and the government and embassy ofPakistanhave no knowledge of the case.”

Law enforcement officials saidPakistanused a network of at least 10 unnamed straw contributors, which Mr. Ahmad helped organize, to make the campaign contributions and donate the bulk of theKashmiriCenter’s annual operating budget. The ISI would reimburse them — or their families inPakistan— for the donations, the officials said.

Most of the straw donors who made contributions to theKashmiriCenterand to politicians in the United States were identified only by code in the court document, though the investigation was continuing and eight F.B.I. field offices executed 17 or 18 search warrants related to other suspected donors, an official said.

The goal of the group, according to internal documents cited by the F.B.I., was to persuade the United States government that it was in its interest to pushIndiato allow a vote inKashmirto decide its future. The group’s strategy was to offset the Indian lobby by targeting members of the Congressional committees that focus on foreign affairs with private briefings and events, staging activities that would draw media attention and otherwise to elevate the issue of Kashmir — the disputed region between India and Pakistan that each country controls in part but claims entirely — in Washington.

The F.B.I. said that there was no evidence that any of the lawmakers who received campaign funds from Pakistan were aware of its origins, and it did not name any of the recipients.

However, a search in Federal Elections Commission databases for contributions by Mr. Fai showed that he has made more than $20,000 in campaign contributions over the past two decades. The bulk of his donations went to two recipients: the National Republican Senatorial Committee and Representative Dan Burton, a Republican from Indiana.

Mr. Fai made numerous — though smaller — contributions to Democrats as well, including to Representatives James P. Moran of Virginia, Dennis J. Kucinich of Ohio and Gregory W. Meeks of New York, and $250 donations to the 2000 and 2008 presidential campaigns of Al Gore and Barack Obama.

Mr. Ahmad also donated to Mr. Burton, records show. For at least 15 years, Mr. Burton has been a champion for Kashmiri causes in Congress, appealing to Presidents Bill Clinton and Obama to get more involved in attempting to mediate a settlement between India and Pakistan over the border region. He has also endorsed allowing the Kashmiri people to vote on their own fate.

Mr. Burton said he was “deeply shocked” by the arrest of Mr. Fai, because he had known him for 20 years and “in that time I had no inkling of his involvement with any foreign intelligence operation and had presumed our correspondence was legitimate.” He said he would donate the funds provided to his campaign to the Boy Scouts of America.

Both Mr. Fai and Mr. Ahmad also donated to Representative Joe Pitts, a Pennsylvania Republican who visited the region in 2001 and 2004, meeting with Pakistani and Indian leaders and calling for a cease-fire. He also introduced a resolution in 2004 calling for President Bush to appoint a special envoy to help negotiate peace.

A spokesman for Mr. Pitts said he had donated $4,000 — an amount equal to the donations his campaign received from the two defendants — to local charities in Pennsylvania on July 19.

Among the evidence that Mr. Fai was working forPakistan, the affidavit said, are annual budget requests he allegedly submitted to his handlers along with lists of accomplishments and strategic-planning documents. Other documents and intercepts showed that they sometimes quarreled over reimbursing him for the costs of trips or about contracts for which he had not gotten advance approval.

The board of the Kashmiri American Council comprises mostly physicians and lawyers from across the United States, and election records show that several board members have made significant donations to lawmakers who have championed peace inKashmir.

Gulam Hassan Butt, a retired California physician and member of the council’s board whose name does not appear in the donor database, said in a phone interview that the council carried out a “regular, honest, open campaign” with lawmakers and the State Department to get the United States to help resolve the Kashmir issue.

He also said he was unaware of any money thatPakistan’s government might have provided to the Kashmiri American Council, but Mr. Fai did not inform board members about all the sources of the council’s revenue: “Where does he get the money?” Mr. Butt said. “I don’t know. Who gives him the money? I don’t know.”

ISI Arrests Doctor Working for the CIA Who Took Osama’s Childrens’ DNA

The CIA organised a fake vaccination program in Abbottabad where it believed Osama Bin Laden was hiding in an elaborate attempt to obtain DNA from the fugitive al-Qaida leader’s family.

As part of extensive preparations for the raid that killed Osama in May, CIA agents recruited a senior Pakistani doctor to organise the vaccine drive in Abbottabad, even starting the “project” in a poorer part of town to make it look more authentic.

The doctor, Shakil Afridi, has since been arrested by the ISI for co-operating with American intelligence agents.

Relations betweenWashingtonandIslamabad, already severely strained by the Osama operation, have deteriorated considerably since then. The doctor’s arrest has exacerbated these tensions. TheUSis understood to be concerned for the doctor’s safety, and is thought to have intervened on his behalf.

The vaccination plan was conceived after American intelligence officers tracked an al-Qaida courier, known as Abu Ahmad al-Kuwaiti, to what turned out to be Osama’s Abbottabad compound last summer in 2010. The agency monitored the compound by satellite and surveillance from a local CIA safe house in Abbottabad, but wanted confirmation that Osama was there before mounting a risky operation inside another country.

DNA from any of the Osama children in the compound could be compared with a sample from his sister, who died in Boston in 2010, to provide evidence that the family was present.

So agents approached Afridi, the health official in charge of Khyber, part of the tribal area that runs along the Afghan border.

The doctor went to Abbottabad in March 2011, saying he had procured funds to give free vaccinations for hepatitis B. Bypassing the management of the Abbottabad health services, he paid generous sums to low-ranking local government health workers, who took part in the operation without knowing about the connection to Osama. Health visitors in the area were among the few people who had gained access to the Osama compound in the past, administering polio drops to some of the children.

Afridi had posters for the vaccination program put up around Abbottabad, featuring a vaccine made by Amson, a medicine manufacturer based on the outskirts ofIslamabad.

In March health workers administered the vaccine in a poor neighbourhood on the edge of Abbottabad called Nawa Sher. The hepatitis B vaccine is usually given in three doses, the second a month after the first. But in April, instead of administering the second dose in Nawa Sher, the doctor returned to Abbottabad and moved the nurses on toBilalTown, the suburb where Osama lived.

It is not known exactly how the doctor hoped to get DNA from the vaccinations, although nurses could have been trained to withdraw some blood in the needle after administrating the drug.

“The whole thing was totally irregular,” said one Pakistani official. “BilalTownis a well-to-do area. Why would you choose that place to give free vaccines? And what is the official surgeon of Khyber doing working in Abbottabad?”

A nurse known as Bakhto, whose full name is Mukhtar Bibi, managed to gain entry to the Osama compound to administer the vaccines. According to several sources, the doctor, who waited outside, told her to take in a handbag that was fitted with an electronic device. It is not clear what the device was, or whether she left it behind. It is also not known whether the CIA managed to obtain any Osama DNA, although one source suggested the operation did not succeed.

Mukhtar Bibi, who was unaware of the real purpose of the vaccination campaign, would not comment on the programme.

Pakistani intelligence became aware of the doctor’s activities during the investigation into the USraid in which Osama was killed on the top floor of the Abbottabad house. Islamabadrefused to comment officially on Afridi’s arrest, but one senior official said: “Wouldn’t any country detain people for working for a foreign spy service?“

The doctor is one of several people suspected of helping the CIA to have been arrested by the ISI, but he is thought to be the only one still in custody.

Pakistan is furious over being kept in the dark about the raid, and theUS is angry that the Pakistani investigation appears more focused on finding out how the CIA was able to track down the al-Qaida leader than on how Osama was able to live in Abbottabad for five years.

The CIA refused to comment on the vaccination plot.

Pakistan Pledge Three Dozen Visas to CIA Officers

Pakistan has pledged to grant more than three dozen visas to CIA officers as part of confidence-building measures following theUSraid killing Osama bin Laden.

An Associated Press report says that the visas are part of an agreement to rebuild counterterrorism efforts by forming what Pakistani officials call a joint intelligence team.

The agreement was reached after talks inIslamabadbetween ISI chief Lt Gen Ahmed Shuja Pasha and CIA officials, including Leon Panetta.

The visas will help replenish CIA staff on the ground, as some staffers were forced to leave when their visas were not renewed in the aftermath of the controversy over CIA contractor Raymond Davis.

There will also be some additional officers allowed in to join the joint intelligence effort to hunt high value al Qaeda targets.

Despite promises from Pakistani officials, the visas have yet to be issued, officials from both sides said. The Pakistanis say it’s simply a matter of time but would not say when they would be given.

CIA Instigating Mutiny in Pakistan Army

By M K Bhadrakumar, a former Indian ambassador

TheUnited Statesis confronting the Pakistani military leadership of General Kayani. An extremely dangerous course to destabilise Pakistanis commencing. Can the outcome be any different than in Iran in 1979? But then, the Americans are like Bourbons; they never learn from their mistakes.

The NYT report quotes US officials not less than 7 times, which is extraordinary, including “an American military official involved withPakistanfor many years”; “a senior American official”, etc. The dispatch is cleverly drafted to convey the impression that a number of Pakistanis have been spoken to, but reading between the lines, conceivably, these could also probably have been indirect attribution by the American sources.

A careful reading, in fact, suggests that the dispatch is almost entirely based on deep briefing by some top US intelligence official with great access to records relating to the most highly sensitive US interactions with the Pak army leadership and who was briefing on the basis of instructions from the highest level of the US intelligence apparatus.

The report no doubt underscores that the US intelligence penetration of the Pak defence forces is deep. It is no joke to get a Pakistani officer taking part in an exclusive briefing by Kayani at the National Defence University to share his notes with the US interlocutors – unless he is their “mole”. This is like a morality play for we Indians, too, where theUSintelligence penetration is ever broadening and deepening. Quite obviously, the birds are coming to roost. Pakistani military is paying the price for the big access it provided to the US to interact with its officer corps within the framework of their so-called “strategic partnership”. The Americans are now literally holding the Pakistani army by its jugular veins. This should serve as a big warning for all militaries of developing countries likeIndia. The NYT story flags in no uncertain terms that although Cold War is over, history has not ended.

What are the objectives behind the NYT story?

Whichever way we look at it, they all are highly diabolic.

One, US is rubbishing army chief Parvez Kayani and ISI head Shuja Pasha who at one time were its own blue-eyed boys and whose successful careers and post-retirement extensions in service the Americans carefully choreographed fostered with a pliant civilian leadership in Islamabad, but now when the crunch time comes, the folks are not “delivering”. In American culture, as they say, there is nothing like free lunch. The Americans are livid that their hefty “investment” has turned out to be a waste in every sense.And.it was a very painstakingly arranged investment, too. In short, the Americans finally realise that they might have made a miscalculation about Kayani when they promoted his career.

Two,USintelligence estimation is that things can only go from bad to worse in US-Pakistan relations from now onward. All that is possible to salvage the relationship has been attempted. John Kerry, Hillary Clinton, Mike Mullen – the so-called “friends of Pakistan” in the Barack Obama administration – have all come to Islamabad and turned on the charm offensive. But nothing worked. Then came CIA boss Leon Panetta with a deal that like Marlon Brando said in the movie Godfather, Americans thought the Pakistanis cannot afford to say ‘No’ to, but to their utter dismay, Kayani showed him the door.

The Americans realise that Kayani is fighting for his own survival – and so is Pasha – and that makes him jettison his “pro-American” mindset and harmonise quickly with the overwhelming opinion within the army, which is that the Americans pose a danger to Pakistan’s national security and it is about time that the military leadership draws a red line. Put simply,Pakistanfears that the Americans are out to grab their nuclear stockpile. Pakistani people and the military expect Kayani to disengage from the US-led Afghan war and instead pursue an independent course in terms of the country’s perceived legitimate interests.

Three, there is a US attempt to exploit the growing indiscipline within the Pak army and, if possible, to trigger a mutiny, which will bog down the army leadership in a serious “domestic” crisis that leaves no time for them for the foreseeable future to play any forceful role in Afghanistan. In turn, it leaves the Americans a free hand to pursue their own agenda. Time is of the essence of the matter and the US desperately wants direct access to the Taliban leadership so as to strike a deal with them without the ISI or Hamid Karzai coming in between.

The prime US objective is that Taliban should somehow come to a compromise with them on the single most crucial issue of permanentUSmilitary bases inAfghanistan. The negotiations over the strategic partnership agreement with Karzai’s government are at a critical point. The Taliban leadership of Mullah Omar robustly opposes theUSproposal to set up American and NATO bases on their country. The Americans are willing to take the Taliban off the UN’s sanctions list and allow them to be part of mainstream Afghan political life, including in the top echelons of leadership, provided Mullah Omar and the Quetta Shura agree to play ball.

TheUStried its damnest to get Kayani to bring the Taliban to the reconciliation path. When these attempts failed, they tried to establish direct contact with the Taliban leadership. But ISI has been constantly frustrating theUSintelligence activities in this direction and reminding theUSto stick to earlier pledges that Pakistan would have a key role in the negotiations with the Taliban. The CIA and Pentagon have concluded that so long as the Pakistani military leadership remains stubborn, they cannot advance their agenda in Afghanistan.

Now, how do you get Kayani and the ISI to back off? The US knows the style of functioning of the Pakistani military. The army chief essentially works within a collegium of the 9 corps commanders. Thus, US has concluded that it also has to tackle the collegium. The only way is to set the army’s house on fire so that the generals get distracted by the fire-dousing and the massive repair work and housecleaning that they will be called upon to undertake as top priority for months if not years to come. To rebuild a national institution like the armed forces takes years and decades.

Four, theUSwon’t mind if Kayani is forced to step aside from his position and the Pakistani military leadership breaks up in disarray, as it opens up windows of opportunities to have Kayani and Pasha replaced by more “dependable” people – Uncle Sam’s own men. There is every possibility that theUShas been grooming its favourites within the Pak army corps for all contingencies.Pakistanis too important as a “key non-NATO ally”. The CIA is greatly experienced in masterminding coup d-etat, including “in-house” coup d’etat. Almost all the best and the brightest Pak army officers have passed through the US military academies at one time or another. Given the sub-continent’s middle class mindset and post-modern cultural ethos, elites in civil or military life take it for granted that US backing is a useful asset for furthering career. The officers easily succumb to US intelligence entrapment. Many such “sleepers” should be existing there within the Pak army officer corps.

The big question remains: has someone in Washington thought through the game plan to tame the Pakistani military? The heart of the matter is that there is virulent “anti-Americanism” within the Pak armed forces. Very often it overlaps with Islamist sympathies. Old-style left wing “anti-Americanism” is almost non-existent in the Pakistani armed forces – as in Ayaz Amir’s time. These tendencies in the military are almost completely in sync with the overwhelming public opinion in the country as well.

Over the past 3 decades at least, Pakistani army officers have come to be recruited almost entirely from the lower middle class – as in our country – and not from the landed aristocracy as in the earlier decades up to the 1970s. These social strata are quintessentially right wing in their ideology, nationalistic, and steeped in religiosity that often becomes indistinguishable from militant religious faith.

Given the overall economic crisis in Pakistan and the utterly discredited Pakistani political class (as a whole) and countless other social inequities and tensions building up in an overall climate of cascading violence and great uncertainties about the future gnawing the mind of the average Pakistani today, a lurch toward extreme right wing Islamist path is quite possible. The ingredients inPakistanare almost nearing those prevailing inIranin the Shah’s era.

The major difference so far has been that Pakistan has an armed forces “rooted in the soil” as a national institution, which the public respected to the point of revering it, which on its part, sincerely or not, also claimed to be the Praetorian Guards of the Pakistani state. Now, in life, destroying comes very easy. Unless the Americans have some very bright ideas about how to go about nation-building in Pakistan, going by their track record in neighbouringAfghanistan, their present course to discredit the military and incite its disintegration or weakening at the present crisis point, is fraught with immense dangers.

The instability in the region may suit the US’ geo-strategy for consolidating its (and NATO’s) military presence in the region but it will be a highly self-centred, almost cynical, perspective to take on the problem, which has dangerous, almost explosive, potential for regional security. Also, who it is that is in charge of the Pakistan policy in Washington, we do not know. To my mind, Obama administration doesn’t have a clue since Richard Holbrooke passed away as to how to handlePakistan. The disturbing news in recent weeks has been that all the old “Pakistanhands” in the USG have left the Obama administration. It seems there has been a steady exodus of officials who knew and understood howPakistanworks, and the depletion is almost one hundred percent. That leaves an open field for the CIA to set the policies.

The CIA boss Leon Panetta (who is tipped as defence secretary) is an experienced and ambitious politico who knows how to pull the wires in the Washington jungle – and, to boot it, he has an Italian name. He is unlikely to forgive and forget the humiliation he suffered in Rawalpindi. The NYT story suggests that it is not in his blood if he doesn’t settle scores with the Rawalpindi crowd. If Marlon Brando were around, he would agree.

Harkatul Mujahedeen was Supporting Osama in Abbottabad

The cellphone of Osama bin Laden’s trusted courier, which was recovered in the raid that killed both men inPakistan in May 2011, contained contacts to a militant group that is a longtime asset ofPakistan’s intelligence agency, senior American officials who have been briefed on the findings say.

The discovery indicates that Osama used the group, Harakat-ul-Mujahedeen, as part of his support network inside the country, the officials and others said. But it also raised tantalizing questions about whether the group and others like it helped shelter and support Osama on behalf ofPakistan’s spy agency, given that it had mentored Harakat and allowed it to operate inPakistan for at least 20 years.

In tracing the calls on the cellphone, American analysts have determined that Harakat commanders had called Pakistani intelligence officials, the senior American officials said. One said they had met. The officials added that the contacts were not necessarily about Osama and his protection and that there was no “smoking gun” showing thatPakistan’s spy agency had protected Osama.

But the cellphone numbers provide one of the most intriguing leads yet in the hunt for the answer to an urgent and vexing question for Washington: How was it that Osama was able to live comfortably for years in Abbottabad, a town dominated by the Pakistani military and only a three-hour drive from Islamabad, the capital?

“It’s a serious lead,” said one American official. “It’s an avenue we’re investigating.”

The revelation also provides a potentially critical piece of the puzzle about Osama’s secret odyssey after he slipped away from American forces in the Tora Bora region ofAfghanistannearly 10 years ago. It may help answer how and why Osama or his protectors chose Abbottabad.

Harakat has especially deep roots in the area around Abbottabad, and the network provided by the group would have enhanced Osama’s ability to live and function in Pakistan. Its leaders have strong ties with both Al Qaeda and Pakistani intelligence, and they can roam widely because they are Pakistanis, something the foreigners who make up Al Qaeda’s ranks cannot do.

Even today, the group’s leader, Maulana Fazlur Rehman Khalil, long one of Osama’s closest Pakistani associates, lives unbothered by Pakistani authorities on the outskirts ofIslamabad.

The senior American officials did not name the commanders whose numbers were in the courier’s cellphone but said that the militants were inSouth Waziristan, where Al Qaeda and other groups had been based for years. Harakat’s network would have allowed Osama to pass on instructions to Qaeda members there and in other parts ofPakistan’s tribal areas, to deliver messages and money or even to take care of personnel matters.

Wielding a Militant Tool

Harakat is one of a host of militant groups set up in the 1980s and early ’90s with the approval and assistance of ISI to fight as proxies inAfghanistan, initially against the Soviets, or againstIndiain the disputedterritoryofKashmir. Like many groups, it has splintered and renamed itself over the years, and because of their overlapping nature, other groups could have been involved in supporting Osama, too. But Harakat, they said, has been a favored tool of the ISI.

Harakat “is one of the oldest and closest allies of Al Qaeda, and they are very, very close to the ISI,” said Bruce O. Riedel, a former Central Intelligence Agency officer and the author of “Deadly Embrace: Pakistan, America, and the Future of the Global Jihad.”

“The question of ISI and Pakistani Army complicity in Osama’s hide-out now hangs like a dark cloud over the entire relationship” between Pakistan and the United States, Mr. Riedel added.

Indeed, suspicions abound that the ISI or parts of it sought to hide Osama, perhaps to keep him as an eventual bargaining chip, or to ensure that billions of dollars in American military aid would flow toPakistanas long as Osama was alive.

Both the chairman of the House Permanent Select Committee on Intelligence, Representative Mike Rogers, Republican of Michigan, and the panel’s ranking Democrat, Representative C. A. Dutch Ruppersberger of Maryland, said that they believed that some members of the ISI or the Pakistani Army, either retired or on active duty, were involved in harboring Osama.

Osama himself had a long history with the ISI, dating to the mujahedeen insurgency that the Americans and Pakistanis supported against the Soviets inAfghanistanin the 1980s.

Two former militant commanders and one senior fighter who have received support from the ISI for years said they were convinced that the ISI played a part in sheltering Osama. Because of their covert existence, they spoke on the condition that their names not be used.

In the spring of 2003, Bin Laden, accompanied by a personal guard unit of Arab and Chechen fighters, arrived unexpectedly at a gathering of 80 to 90 militants at a village in the Shawal mountain range of North Waziristan, inPakistan’s tribal areas, the former commander said. He met Bin Laden briefly inside a house; he said he knew it was him because they had met before, inAfghanistanbefore the Sept. 11, 2001, terrorist attacks.

The encounter in North Waziristanoccurred before the American campaign of drone aircraft strikes, which began in 2004, made it unsafe for militants to gather in the area in large numbers. For about three years before the American drone campaign, Bin Laden was moving from place to place inPakistan’s mountainous tribal areas, the commander said.

TheUnited Stateshad small Special Operations units and C.I.A. operatives working with Pakistani security forces to track Qaeda members at that time. At some point Bin Laden went deeper underground. That is when the commander speculated that the Qaeda leader was moved to a safe house in a city, though he did not say he knew that Bin Laden had gone to Abbottabad.

He and the other commander, who spent 10 years with Harakat, offered no proof of their belief that Bin Laden was under Pakistani military protection. But their views were informed by their years of work with the ISI and their knowledge of how the spy agency routinely handled militant leaders it considered assets — placing them under protective custody in cities, often close to military installations.

The treatment amounts to a kind of house arrest, to ensure both the security of the asset and his low profile to avoid embarrassment to his protectors.

Art Keller, a former C.I.A. officer who worked inPakistanin 2006, said he had heard rumors after he leftPakistanin 2007 that Harakat was providing “background” assistance with logistics in moving and maintaining the Qaeda leader inPakistan. That did not necessarily mean that members of the group were aware of the role they played or knew of Bin Laden’s whereabouts, another American intelligence official said, speaking on the condition of anonymity because of the nature of his work.

It remains unclear how Bin Laden arrived in Abbottabad, where American officials say he and his family lived for five years, beginning in 2006. The city is home to one of the nation’s top military academies, which sits less than a mile from the compound where Bin Laden was killed.

It is also a transit point for militants moving betweenKashmirand the tribal areas. The region is the prime recruitment base of Harakat, whose training camps and other facilities still exist nearby in Mansehra.

Through the late 1990s, Harakat collaborated closely with the Taliban and Al Qaeda, sharing training camps and channeling foreign fighters to Qaeda camps inAfghanistan.

The group’s leader, Mr. Khalil, was a co-signer of Bin Laden’s 1998 edict ordering attacks againstAmerica. The group even organized press trips for journalists to see Bin Laden inAfghanistanbefore 9/11 and was used to pass messages to him, said Asad Munir, a retired brigadier and former intelligence official.

Such were the links between the groups that when theUnited Statesfired cruise missiles at Bin Laden’s camps inAfghanistan, after the 1998 American Embassy bombings inTanzaniaandKenya, 11 Harakat fighters were killed. Some of the group’s fighters were also killed in the bombings of one of Bin Laden’s bases inAfghanistanat the start of the American invasion in October 2001.

Driven Underground

Under strong American pressure, Harakat and similar groups were officially banned and driven underground by the government of Musharraf in 2002. Harakat just renamed itself and continued to run camps unencumbered by Pakistani authorities and to train militants, some of whom have been caught while fighting American and NATO forces inAfghanistan.

After 2007, many of its fighters left to join the Taliban, but its leadership and network have remained intact, if reduced, the commanders said. Indeed, Bin Laden’s courier appears to have used a camp in Mansehra that belonged to a Harakat splinter group, Jaish-e-Muhammad, as a transit stop, said an American government official familiar with the analysis of the Bin Laden material.

The Pakistani Army continued its links with the Harakat leadership, in particular Mr. Khalil, Pakistani officials and analysts said. In 2007, Mr. Khalil was used by the Musharraf government as a member of a group of clerics who tried to negotiate an end to a siege by militants at the Red Mosque inIslamabad.

“They can find him when they want him,” said Muhammad Amir Rana, the director of the Pak Institute of Peace Studies, who has written a book on militant groups.

What role if any Mr. Khalil may have played in helping Bin Laden in Abbottabad, or whether he even knew he was living there, is still not clear. It is also the case that hard-liners within the ranks of his organization may had become disillusioned with their ISI handlers over the years, broke from them and operated more independently.

Another Pakistani militant leader closely connected to Bin Laden is Qari Saifullah Akhtar, the leader of Harakat-ul-Jihad-al-Islami. Mr. Akhtar stopped in South Waziristan on the way toAfghanistanjust months ago, a militant interviewed by phone said.

The presence in Waziristan of Mr. Akhtar — who is wanted in connection with the attack that killed Benazir Bhutto, a former prime minister, in 2007 — demonstrated that he could still move freely without ISI interference.

A report by the Pakistani Interior Ministry said that Mr. Akhtar had visited Bin Laden in August 2009 near the border withAfghanistanto discuss jihadist operations againstPakistan, according to an account that was published in the Pakistani newspaper The Daily Times in 2010.

It is the only recorded episode showing that Bin Laden’s presence insidePakistanwas known to Pakistani intelligence, until the American raid that killed him.

Why Has ISI Arrested CIA Informants?

by Eric Schmitt & Mark Mazzetti/ NYT

ISI has arrested some of the Pakistani informants who fed information to the CIA in the months leading up to the raid that led to the death of Osama bin Laden, according to American officials. Pakistan’s detention of five CIA informants, including a Pakistani Army major who officials said copied the license plates of cars visiting Bin Laden’s compound in Abbottabad, in the weeks before the raid, is the latest evidence of the fractured relationship between theUnited States andPakistan. It comes at a time when the Obama administration is seekingPakistan’s support in brokering an endgame in the war in neighboringAfghanistan.

At a closed briefing last week, members of the Senate Intelligence Committee asked Michael J. Morell, the deputy C.I.A. director, to rate Pakistan’s cooperation with the United States on counterterrorism operations, on a scale of 1 to 10.  “Three,” Mr. Morell replied, according to officials familiar with the exchange.

The fate of the CIA informants arrested in Pakistanis unclear, but American officials said that the CIA director, Leon E. Panetta, raised the issue when he travelled to Islamabad last week to meet with Pakistani military and intelligence officers.

Some in Washington see the arrests as illustrative of the disconnect between Pakistani and American priorities at a time when they are supposed to be allies in the fight against Al Qaeda — instead of hunting down the support network that allowed Bin Laden to live comfortably for years, the Pakistani authorities are arresting those who assisted in the raid that killed the world’s most wanted man.

The Bin Laden raid and more recent attacks by militants inPakistan have been blows to the country’s military, a revered institution in the country. Some officials and outside experts said the military is mired in its worst crisis of confidence in decades.

American officials cautioned that Mr. Morell’s comments about Pakistani support was a snapshot of the current relationship, and did not represent the administration’s overall assessment.

“We have a strong relationship with our Pakistani counterparts and work through issues when they arise,” said Marie E. Harf, a C.I.A. spokeswoman. “Director Panetta had productive meetings last week inIslamabad. It’s a crucial partnership, and we will continue to work together in the fight against Al Qaeda and other terrorist groups who threaten our country and theirs.”

Husain Haqqani,Pakistan’s ambassador to theUnited States, said in a brief telephone interview that the C.I.A. and the Pakistani spy agency “are working out mutually agreeable terms for their cooperation in fighting the menace of terrorism. It is not appropriate for us to get into the details at this stage.”

Over the past several weeks the Pakistani military has been distancing itself from American intelligence and counterterrorism operations against militant groups in Pakistan. This has angered many in Washington who believe that Bin Laden’s death has shaken Al Qaeda and that there is now an opportunity to further weaken the terrorist organization with more raids and armed drone strikes.

But in recent months, dating approximately to when a C.I.A. contractor killed two Pakistanis on a street in the eastern city of Lahore in January, American officials said that Pakistani spies from the Directorate for ISI, have been generally unwilling to carry out surveillance operations for the CIA. The Pakistanis have also resisted granting visas allowing American intelligence officers to operate inPakistan, and have threatened to put greater restrictions on the drone flights.

It is the future of the drone program that is a particular worry for the C.I.A. American officials said that during his meetings in Pakistan last week, Mr. Panetta was particularly forceful about trying to get Pakistani officials to allow armed drones to fly over even wider areas in the northwest tribal regions. But the C.I.A. is already preparing for the worst: relocating some of the drones fromPakistanto a base in Afghanistan, where they can take off and fly east across the mountains and into the tribal areas, where terrorist groups find safe haven.

Another casualty of the recent tension is an ambitious Pentagon program to train Pakistani paramilitary troops to fight Al Qaeda and the Taliban in those same tribal areas. That program has ended, both American and Pakistani officials acknowledge, and the last of about 120 American military advisers have left the country.

American officials are now scrambling to find temporary jobs for about 50 Special Forces support personnel who had been helping the trainers with logistics and communications. Their visas were difficult to obtain and officials fear if these troops are sent home,Pakistanwill not allow them to return.

In a sign of the growing anger on Capitol Hill, Representative Mike Rogers, a Michigan Republican who leads the House Intelligence Committee, said Tuesday that he believed elements of the ISI and the military had helped protect Bin Laden.

Mr Rogers, who met with senior security officials in Pakistan last week, said he had no evidence that senior Pakistani military or civilian leaders were complicit in sheltering Bin Laden. And he did not offer any proof to support his assertion, saying only his accusation was based on “information that I’ve seen.”He warned that both lawmakers and the Obama administration could end up putting more restrictions on the $2 billion in American military aid received annually by Pakistan. He also called for “benchmarks” in the relationship, including more sharing of information about militant activities inKarachi,Lahore and elsewhere and more American access to militants detained in Pakistan.

American military commanders inAfghanistanappear cautiously optimistic that they are making progress in pushing the Taliban from its strongholds in that country’s south, but many say a significant American military withdrawal can occur only if the warring sides inAfghanistanbroker some kind of peace deal.

But theUnited Statesis reliant onPakistanto apply pressure on Taliban leaders, over whom they have historically had great influence.

For now, at least,America’s relationship with Pakistan keeps getting tripped up. When he visitedPakistan, Mr. Panetta offered evidence of collusion between Pakistani security officials and the militants staging attacks inAfghanistan.

American officials said Mr. Panetta presented satellite photographs of two bomb-making factories that American spies several weeks ago had asked the ISI to raid. When Pakistani troops showed up days later, the militants were gone, causing American officials to question whether the militants had been warned by someone on the Pakistani side.

Shortly after the failed raids, the Defense Department put a hold on a $300 million payment reimbursingPakistanfor the cost of deploying more than 100,000 troops along the border with Afghanistan, two officials said.  The Pentagon declined to comment on the payment, except to say it was “continuing to process several claims.”

 

Osama Debacle Will Compel Pakistan’s Military Leadership to Demonstrate a Greater Commitment to Fighting Al-Qaeda

Stung by the embarrassment of the discovery and death of Osama bin Laden in Abbottabad late Sunday night, May 1,Pakistan’s powerful military establishment is under pressure to make changes in its relationship with key allies and in its fight against terrorism.

After three days of sedulous silence on the matter, the military and intelligence leadership on May 5, shared its perspective on the Abbottabad debacle. The rare closed-door briefing was prompted by a desire to challenge an emerging global narrative that incriminated Pakistan’s security establishment in bin Laden’s ability to elude capture.

General Kayani reiterated at the briefing that Pakistan had not been informed of the raid until it was over. The first communication from the U.S.was a phone call at around 5 a.m.Pakistantime from Admiral Mike Mullen, Chairman of the Joint Chiefs of Staff. Kayani congratulated Mullen on the mission’s success but pleaded that President Barack Obama should refrain from “negative remarks” about Pakistan in his planned address. He was pleased that Obama’s live TV announcement avoided criticism ofPakistan.

Kayani’s first indication of the raid came earlier, however, with the news of a helicopter crashing and exploding, which was covered by local news media in Abbottabad. The general knew it wasn’t a Pakistani helicopter — “We don’t fly at night,” he told reporters gathered at the military’s headquarters inRawalpindi. Kayani picked up the phone and ordered his air force to “scramble the jets.” Pakistani military analysts say an order to scramble jets is an authorization to shoot down anything in the sky. But by the time two F-16s reached the scene, the Americans had left.

Kayani responded to Pakistani concerns over how the U.S.helicopters had entered Pakistani airspace undetected by attributing the entry to technological advantages.

The most damaging accusation against the Pakistani military, of course, is that it must have known Osama was hiding in the small garrison town where army personnel demand identification at frequent checkpoints.

Kayani was adamant that the Pakistanis had no idea that Osama was hiding in Abbottabad. “We had no clear, actionable information on Osama,” he told the journalists. “If we had it, we would have acted ourselves. No one would have questioned our performance for 10 years. It would have raised our international prestige.”

Kayani’s argument is supported by some senior Western diplomats in Islamabad, who say that there is no conclusive evidence of Pakistani complicity. Nor have Washington’s statements alleged complicity, despite suspicions. Diplomats do not rule out the possibility that junior intelligence officers may have been involved, however. Instead of focusing on whether Pakistan was either complicit or incompetent, the explanation may lie in its lack of focus or effort. In recent years, Pakistan has chiefly concentrated on the threat from the Pakistani Taliban, to the neglect of those posed by al-Qaeda and the Afghan Taliban.

The Abbottabad area, Kayani told the briefing, had been of interest toPakistan’s security establishment since at least 2004. There was no suspicion involving the compound, though, and he emphasized that the intelligence gathered had been diffuse.

Suspicions about Abbottabad were first raised when intercept equipment picked up phone calls in Arabic toSaudi Arabiaon the subject of finances. That information,Pakistan’s military leadership says, was shared with theU.S.At some point, the CIA shut down its communication with the ISI. No intelligence agency shares 100% of its intelligence with another country, said Kayani, himself a former ISI chief.

Kayani said that in his ISI role, he was responsible for tracking down Abu Faraj al-Libbi, a senior al-Qaeda member who lived in Abbottabad in 2003 and was arrested the following year in Mardan. Western diplomats and analysts say that Pakistan’s success in capturing several al-Qaeda members has been driven byU.S.intelligence.

Al-Qaeda leaders Khalid Sheikh Mohammed and Ramzi Binalshibh and Afghan Taliban commander Mullah Baradar were all seized in joint operations.

When it came to Osama, however,U.S.officials feared that cooperation could compromise the operation.

While Pakistani Foreign Secretary Salman Bashir had earlier spoken of “strategic convergence” between Islamabad and Washington,Pakistan’s intelligence chief chose to be less emollient. Sitting near Kayani, Lieut. General Ahmed Shuja Pasha said that despite extensive mutual assistance between the CIA and the ISI,Pakistanhad made its interests clear toWashington. Pasha said he had made clear toWashingtonthat if theU.S.were deemed to be acting againstPakistan’s interests, “We’ll not help you — we’ll resist you.”

The consensus among diplomats and analysts is that the Osama debacle will compelPakistan’s military leadership to demonstrate a greater commitment to fighting al-Qaeda. Pakistani leaders have said that neither will they tolerate, nor can they afford, further similar raids — for example, to seize al-Qaeda No. 2 Ayman al-Zawahiri or Taliban leader Mullah Omar. That said, it is fair to assume that the ISI will seek to avoid that possibility by intensifying its efforts to find bin Laden’s deputy. At the same time,Pakistancan be expected to assert itself in ways thatWashingtonwill not like.

Embarrassment over Osama’s presence in Abbottabad notwithstanding, the Pakistani security establishment is angry at what it views as the firstU.S.invasion of a nuclear-armed ally. It fears that neighboringIndiamay be smiling at the vulnerability demonstrated by the American raid, and the resulting indignity is hard to swallow. The U.S. Army has decided to “reduce the strength ofU.S.military personnel inPakistanto the minimum essential,” it said in a statement on May 5. At the closed-door briefing, Pasha indignantly claimed that his own ISI was on the verge of being “outnumbered” by foreign agents. Still, the bin Laden episode limits the security establishment’s room to maneuver in several ways.

Until now,Pakistan’s civilian government has sat silently by, watching the military make the key decisions on national security and foreign policy and even extend its control of certain sectors of the economy. A public long accustomed to muffling its criticism of the army has largely acquiesced. Now, for the first time in several years, many are prepared to openly blame the military for a humiliation some are comparing to the fall of Dhaka in 1971, when Pakistan lost control of what is now Bangladesh. Suddenly, the civilian government looks more resilient. And the military is in trouble not only withWashingtonbut also with another key ally,Saudi Arabia, which will not be pleased that its most determined enemy was found inPakistan. The raid in Abbottabad has produced a moment of rare vulnerability in a military establishment that had long beenPakistan’s strongest power center.

How Did the Americans Find Osama?

For years, the agonizing search for Osama Bin Laden kept coming up empty. Then last July, Pakistanis working for the CIA drove up behind a white Suzuki navigating the bustling streets nearPeshawar, and wrote down the car’s license plate.

The man in the car was Osama’s most trusted courier, and over the next month CIA operatives would track him throughout centralPakistan. Ultimately, administration officials said, he led them to a sprawling compound at the end of a long dirt road and surrounded by tall security fences in a wealthy hamlet 35 miles fromIslamabad.

On a moonless night eight months later, 79 American commandos in four helicopters descended on the compound. Shots rang out. A helicopter stalled and would not take off. Pakistani authorities, kept in the dark by their allies in Washington, scrambled forces as the American commandos rushed to finish their mission and leave before a confrontation. Of the five dead, one was a tall, bearded man with a bloodied face and a bullet in his head. A member of the Navy Seals snapped his picture with a camera and uploaded it to analysts who fed it into a facial recognition program.

And just like that, history’s most expansive, expensive and exasperating manhunt was over. The inert frame ofOsama,America’s enemy No. 1, was placed in a helicopter for burial at sea, never to be seen or feared again. A nation that spent a decade tormented by its failure to catch the man responsible for nearly 3,000 fiery deaths in New York, outside Washington and Pennsylvania on Sept. 11, 2001, at long last had its sense of finality, at least in this one difficult chapter.

The raid was the culmination of years of painstaking intelligence work, including the interrogation of CIA detainees in secret prisons inEastern Europe, where sometimes what was not said was as useful as what was. Intelligence agencies eavesdropped on telephone calls and e-mails of the courier’s Arab family in a Persian Gulf state and pored over satellite images of the compound in Abbottabad to determine a “pattern of life” that might decide whether the operation would be worth the risk.

As more than a dozen White House, intelligence and Pentagon officials described the operation, the past few weeks were a nerve-racking amalgamation of what-ifs and negative scenarios. “There wasn’t a meeting when someone didn’t mention ‘Black Hawk Down,’ ” a senior administration official said, referring to the disastrous 1993 battle in Somalia in which two American helicopters were shot down and some of their crew killed in action. The failed mission to rescue hostages inIranin 1980 also loomed large.

Administration officials split over whether to launch the operation, whether to wait and continue monitoring until they were more sure that Osama was really there, or whether to go for a less risky bombing assault. In the end, President Obama opted against a bombing that could do so much damage it might be uncertain whether Osama was really hit and chose to send in commandos. A “fight your way out” option was built into the plan, with two helicopters following the two main assault copters as backup in case of trouble.

On May 1 afternoon, as the helicopters raced over Pakistani territory, the president and his advisers gathered in the Situation Room of the White House to monitor the operation as it unfolded. Much of the time was spent in silence. Mr. Obama looked “stone faced,” one aide said. Vice President Joseph R. Biden Jr. fingered his rosary beads. “The minutes passed like days,” recalled John O. Brennan, the White House counter terrorism chief.

The code name for Osama was “Geronimo.” The president and his advisers watched Leon E. Panetta, the CIA director, on a video screen, narrating from his agency’s headquarters across the Potomac River what was happening in farawayPakistan.

“They ’ve reached the target,” he said.

Minutes passed.

“We have a visual on Geronimo,” he said.

A few minutes later: “Geronimo EKIA.”

Enemy Killed In Action. There was silence in the Situation Room.

Finally, the president spoke up.

“We got him.”

Years before the Sept. 11 attacks transformed Osama into the world’s most feared terrorist, the CIA had begun compiling a detailed dossier about the major players inside his global terror network.

It wasn’t until after 2002, when the agency began rounding up Qaeda operatives — and subjecting them to hours of brutal interrogation sessions in secret overseas prisons — that they finally began filling in the gaps about the foot soldiers, couriers and money men Osama relied on.

Prisoners in American custody told stories of a trusted courier. When the Americans ran the man’s pseudonym past two top-level detainees — the chief planner of the Sept. 11 attacks, Khalid Shaikh Mohammed; and Al Qaeda’s operational chief, Abu Faraj al-Libi — the men claimed never to have heard his name. That raised suspicions among interrogators that the two detainees were lying and that the courier probably was an important figure.

As the hunt for Osama continued, the spy agency was being buffeted on other fronts: the botched intelligence assessments about weapons of mass destruction leading up to the Iraq War, and the intense criticism for using waterboarding and other extreme interrogation methods that critics said amounted to torture.

By 2005, many inside the CIA had reached the conclusion that the Osama hunt had grown cold, and the agency’s top clandestine officer ordered an overhaul of the agency’s counterterrorism operations. The result was Operation Cannonball, a bureaucratic reshuffling that placed more CIA case officers on the ground in Pakistan and Afghanistan.

With more agents in the field, the CIA finally got the courier’s family name. With that, they turned to one of their greatest investigative tools — the National Security Agency began intercepting telephone calls and e-mail messages between the man’s family and anyone insidePakistan. From there they got his full name.

In July 2010, Pakistani agents working for the CIA spotted him driving his vehicle nearPeshawar. When, after weeks of surveillance, he drove to the sprawling compound in Abbottabad, American intelligence operatives felt they were onto something big, perhaps even Osama himself. It was hardly the spartan cave in the mountains that many had envisioned as his hiding place. Rather, it was a three-story house ringed by 12-foot-high concrete walls, topped with barbed wire and protected by two security fences. He was, said Mr. Brennan, the White House official, “hiding in plain sight.”

Back in Washington, Mr. Panetta met with Mr. Obama and his most senior national security aides, including Mr. Biden, Secretary of State  Clinton and Defense Secretary Robert M. Gates. The meeting was considered so secret that White House officials didn’t even list the topic in their alerts to each other.

That day, Mr. Panetta spoke at length about Osama and his presumed hiding place.

“It was electric,” an administration official who attended the meeting said. “For so long, we’d been trying to get a handle on this guy. And all of a sudden, it was like, wow, there he is.”

There was guesswork about whether Osama was indeed inside the house. What followed was weeks of tense meetings between Mr. Panetta and his subordinates about what to do next.

While Mr Panetta advocated an aggressive strategy to confirm Osama’s presence, some CIA clandestine officers worried that the most promising lead in years might be blown if bodyguards suspected the compound was being watched and spirited the Qaeda leader out of the area.

For weeks last fall, spy satellites took detailed photographs, and the N.S.A. worked to scoop up any communications coming from the house. It wasn’t easy: the compound had neither a phone line nor Internet access. Those inside were so concerned about security that they burned their trash rather than put it on the street for collection.

In February, Mr. Panetta called Vice Adm. William H. McRaven, commander of the Pentagon’s Joint Special Operations Command, to CIA headquarters inLangley,Va., to give him details about the compound and to begin planning a military strike.

Admiral McRaven, a veteran of the covert world who had written a book on American Special Operations, spent weeks working with the C.I.A. on the operation, and came up with three options: a helicopter assault using American commandos, a strike with B-2 bombers that would obliterate the compound, or a joint raid with Pakistani intelligence operatives who would be told about the mission hours before the launch.

On March 14, Mr. Panetta took the options to the White House. CIA officials had been taking satellite photos, establishing what Mr. Panetta described as the habits of people living at the compound. By now evidence was mounting that Osama was there.

The discussions about what to do took place as American relations with Pakistan were severely strained over the arrest of Raymond A. Davis, the C.I.A. contractor imprisoned for shooting two Pakistanis on a crowded street inLahorein January. Some of Mr. Obama’s top aides worried that any military assault to capture or kill Osama might provoke an angry response fromPakistan’s government, and that Mr. Davis could end up dead in his jail cell. Mr. Davis was ultimately released on March 16, giving a freer hand to his colleagues.

On March 22, the president asked his advisers their opinions on the options.

Mr Gates was skeptical about a helicopter assault, calling it risky, and instructed military officials to look into aerial bombardment using smart bombs. But a few days later, the officials returned with the news that it would take some 32 bombs of 2,000 pounds each. And how could the American officials be certain that they had killed Osama?

“It would have created a giant crater, and it wouldn’t have given us a body,” said one American intelligence official.

A helicopter assault emerged as the favored option. The Navy Seals team that would hit the ground began holding dry runs at training facilities on both American coasts, which were made up to resemble the compound. But they were not told who their target might be until later.

Last Thursday, the day after the president released his long-form birth certificate — such “silliness,” he told reporters, was distracting the country from more important things — Mr. Obama met again with his top national security officials.

Mr. Panetta told the group that the CIA had “red-teamed” the case — shared their intelligence with other analysts who weren’t involved to see if they agreed that Osama was probably in Abbottabad. They did. It was time to decide.

Around the table, the group went over and over the negative scenarios. There were long periods of silence, one aide said. And then, finally, Mr. Obama spoke: “I’m not going to tell you what my decision is now — I’m going to go back and think about it some more.” But he added, “I’m going to make a decision soon.”

Sixteen hours later, he had made up his mind. Early the next morning, four top aides were summoned to the White House Diplomatic Room. Before they could brief the president, he cut them off. “It’s a go,” he said. The earliest the operation could take place was Saturday, but officials cautioned that cloud cover in the area meant that Sunday was much more likely.

The next day, Mr. Obama took a break from rehearsing for the White House Correspondents Dinner that night to call Admiral McRaven, to wish him luck.

On Sunday, White House officials canceled all West Wing tours so unsuspecting tourists and visiting celebrities wouldn’t accidentally run into all the high-level national security officials holed up in the Situation Room all afternoon monitoring the feeds they were getting from Mr. Panetta. A staffer went to Costco and came back with a mix of provisions — turkey pita wraps, cold shrimp, potato chips, soda.

At 2:05 p.m., Mr. Panetta sketched out the operation to the group for a final time. Within an hour, the CIA director began his narration, via video from Langley. “They’ve crossed intoPakistan,” he said.

The commando team had raced into the Pakistani night from a base in Jalalabad, just across the border inAfghanistan. The goal was to get in and get out before Pakistani authorities detected the breach of their territory by what were to them unknown forces and reacted with possibly violent results.

InPakistan, it was just past midnight on Monday morning, and the Americans were counting on the element of surprise. As the first of the helicopters swooped in at low altitudes, neighbors heard a loud blast and gunshots. A woman who lives two miles away said she thought it was a terrorist attack on a Pakistani military installation. Her husband said no one had any clue Osama was hiding in the quiet, affluent area. “It’s the closest you can be toBritain,” he said of their neighborhood.

The Seal team stormed into the compound — the raid awakened the group inside, one American intelligence official said — and a firefight broke out. One man held an unidentified woman living there as a shield while firing at the Americans. Both were killed. Two more men died as well, and two women were wounded. American authorities later determined that one of the slain men was Osama’s son, Hamza, and the other two were the courier and his brother.

The commandos found Osama on the third floor, wearing the local loose-fitting tunic and pants known as a shalwar kameez, and officials said he resisted before he was shot above the left eye near the end of the 40-minute raid. The American government gave few details about his final moments. “Whether or not he got off any rounds, I frankly don’t know,” said Mr. Brennan, the White House counterterrorism chief. But a senior Pentagon official, briefing on the condition of anonymity, said it was clear Osama “was killed byU.S.bullets.”

American officials insisted they would have taken Osama into custody if he did not resist, although they considered that likelihood remote. “If we had the opportunity to take Osama alive, if he didn’t present any threat, the individuals involved were able and prepared to do that,” Mr. Brennan said.

One of Osama’s wives identified his body, American officials said. A picture taken by a Seals commando and processed through facial recognition software suggested a 95 percent certainty that it was Osama. Later, DNA tests comparing samples with relatives found a 99.9 percent match.

But the Americans faced other problems. One of their helicopters stalled and could not take off. Rather than let it fall into the wrong hands, the commandos moved the women and children to a secure area and blew up the malfunctioning helicopter.

By that point, though, the Pakistani military was scrambling forces in response to the incursion into Pakistani territory. “They had no idea about who might have been on there,” Mr. Brennan said. “Thankfully, there was no engagement with Pakistani forces.”

As they took off at 1:10 a.m. local time, taking a trove of documents and computer hard drives from the house, the Americans left behind the women and children. A Pakistani official said nine children, from 2 to 12 years old, are now in Pakistani custody.

The Obama administration had already determined it would follow Islamic tradition of burial within 24 hours to avoid offending devout Muslims, yet concluded Osama would have to be buried at sea, since no country would be willing to take the body. Moreover, they did not want to create a shrine for his followers.

So the Qaeda leader’s body was washed and placed in a white sheet in keeping with tradition.  On the aircraft carrier Carl Vinson, it was placed in a weighted bag as an officer read prepared religious remarks, which were translated into Arabic by a native speaker.

The body then was placed on a prepared flat board and eased into the sea. Only a small group of people watching from one of the large elevator platforms that move aircraft up to the flight deck were witness to the end of America’s most wanted fugitive.

Appointment of General Petraeus as CIA Director irks ISI

The appointment of Gen. David H. Petraeus as director of the CIA puts him more squarely than ever in conflict with Pakistan, whose military leadership does not regard him as a friend and where he will now have direct control over the armed drone campaign that the Pakistani military says it wants stopped.

Pakistani and American officials said that General Petraeus’s selection could further inflame relations between the two nations, which are already at one of their lowest points, with recriminations over myriad issues aired publicly like never before.

The usually secretive leader of the Pakistani Army, Gen. Kayani, has made little secret of his distaste for General Petraeus, calling him a political general.

General Petraeus has privately expressed outrage at what American officials say is the Pakistani main spy agency’s most blatant support yet for fighters based in Pakistan who are carrying out attacks against American troops in Afghanistan.

Officials on both sides say they expect the two nations’ relationship to become increasingly adversarial as they maneuver the endgame in Afghanistan, where Pakistan and the United States have deep — and conflicting — security interests.

Repairing the frayed ties between the C.I.A. and the ISI will be difficult, American officials say.

In its current form, the relationship is almost unworkable. There has to be a major restructuring.

The ISI jams the C.I.A. all it wants and pays no penalties.

One American military official sought to play down the animosity with Pakistani officials, noting that the general had regularly met with the Pakistanis for nearly three years. Still, the official acknowledged that with General Petraeus leading the C.I.A., “the pressure may be more strategic, deliberate and focused — to the extent that it can be.”

A Pakistani official described the mounting tensions as a game of “brinkmanship,” with both Adm. Mike Mullen, who as chairman of the Joint Chiefs of Staff has been the Obama administration’s point man on Pakistan policy, and General Kayani growing impatient because they have little to show for the many hours they have invested during more than two dozen visits over the past three years.

Admiral Mullen surprised Pakistani officials by publicly accusing the ISI of sheltering fighters from the Haqqani network, a Taliban ally that has long served as a proxy forPakistan’s military and intelligence establishment inAfghanistan. American commanders in eastern Afghanistan say they have killed or captured more than 5,000 militants in the past year, but fighters continue to pour across the border from sanctuaries inPakistan to Paktia, Khost and Paktika Provinces inAfghanistan.

In a private meeting inIslamabadin April 2011, Admiral Mullen told General Kayani that the C.I.A. would not reduce the drone strikes until Pakistan launched a military operation against the Haqqani network inPakistan’s tribal areas.

Pakistan’s military and its intelligence agency are increasingly embarrassed by theUnited States’ drone campaign, which they publicly condemn but quietly allow. They have asked the C.I.A. to remove its personnel from Shamsi air base, about 200 miles southwest ofQuetta, where some of the drones are based, a senior American official said.

The withdrawal has not occurred but is expected soon. The drone attacks would then be flown out of Afghanistan, where some of them are already based, the official said.

There have also been sharp disagreements over a proposed code of conduct that would define what American soldiers and intelligence agents can do in Pakistani territory, a Pakistani official said. The Pakistanis have, for now, dropped the idea of such an accord, fearing that the Americans are looking for “legal cover” for intelligence operatives like Raymond A. Davis, the C.I.A. contractor who killed two Pakistanis in January, a Pakistani official said.

“The relationship between the two countries is tense right now,” said Representative William M. Thornberry ofTexas, a senior Republican on the House Armed Services Committee, who visitedPakistanlast week. “And thePakistangovernment fuels the anti-American public opinion to increase pressure on us.”

Newly disclosed documents obtained by WikiLeaks have also stoked tensions. One of them, from the prison at Guantánamo Bay, Cuba, lists the ISI along with numerous militant groups as allies of Al Qaeda and the Taliban, an indication of how deep American suspicions run when it comes to Pakistani intelligence. The document is undated but appears to be from 2007 or 2008.

Tensions over issues big and small — like accounting for American grants to the Pakistani military and the failure of theUnited Statesto deliver helicopters that would help in counterterrorism efforts — clouded the hastily arranged alliance from the start, he said.

But now the collision of interests over how to end the war inAfghanistan, and the bitterness over the Davis affair, have exposed deep-seated differences, he said.

The drone campaign, which the C.I.A. has run against militants inPakistan’s tribal areas since 2004, will now become the preserve of General Petraeus, and it has moved to center stage, at least for the Pakistanis. Since Mr. Davis’s release from custody inPakistanafter the killings, the C.I.A. has carried out three drone attacks, each one seemingly tied to sensitive events in the United States-Pakistan relationship and aimed at Afghan Taliban militants thatPakistanshelters.

Another former Pakistani general who speaks to General Kayani said he believed that the Pakistan Army’s leader had concluded that the drone campaign should end because it hurt the army’s reputation among the Pakistani public. Those being killed by the drones are of midlevel or even lesser importance, the general said.

The Americans say the drones are more important than ever as a tool to stanch the flow of Taliban foot soldiers coming across the border to fight American and NATO forces.

ISI Clashes with the CIA

Pakistan has demanded that the United States steeply reduce the number of Central Intelligence Agencyoperatives and Special Operations forces working in Pakistan, and that it halt C.I.A. drone strikes aimed at militants in northwest Pakistan. The request was a sign of the near collapse of cooperation between the two testy allies.

Pakistani and American officials said in interviews that the demand that the United States scale back its presence was the immediate fallout from the arrest in Pakistan of Raymond A. Davis, a C.I.A. security officer who killed two men in January during what he said was an attempt to rob him.

In all, about 335 American personnel — C.I.A. officers and contractors and Special Operations forces — were being asked to leave the country, said a Pakistani official closely involved in the decision.

It was not clear how many C.I.A. personnel that would leave behind; the total number in Pakistan has not been disclosed. But the cuts demanded by the Pakistanis amounted to 25 to 40 percent of United States Special Operations forces in the country, the officials said. The number also included the removal of all the American contractors used by the C.I.A. in Pakistan.

The demands appeared severe enough to badly hamper American efforts — either through drone strikes or Pakistani military training — to combat militants who use Pakistan as a base to fight American forces in Afghanistan and plot terrorist attacks abroad.

The reductions were personally demanded by the chief of the Pakistani Army, Gen. Kayani, said Pakistani and American officials, who requested anonymity while discussing the delicate issue.

The scale of the Pakistani demands emerged as Lt. Gen. Ahmed Shuja Pasha, the head of ISI arrived in Washington on Monday for nearly four hours of meetings with the C.I.A. director, Leon E. Panetta, and Adm. Mike Mullen, the chairman of the Joint Chiefs of Staff.

Two senior American officials said afterward that General Pasha did not make any specific requests for reductions of C.I.A. officers, contractors or American military personnel in Pakistan at the meetings.

“There were no ultimatums, no demands to withdraw tens or hundreds of Americans from Pakistan,” said one of the officials, who spoke on the condition of anonymity because of the tensions between the two spy services.

A C.I.A. spokesman, George Little, called the meetings “productive” and said the relationship between the two services “remains on solid footing.”

The meetings were part of an effort to repair the already tentative and distrustful relations between the spy agencies. Those ties plunged to a new low as a result of the Davis episode, which has further exposed the divergence in Pakistani and American interests as the endgame in Afghanistan draws closer.

The Pakistani Army firmly believes that Washington’s real aim in Pakistan is to strip the nation of its prized nuclear arsenal, which is now on a path to becoming the world’s fifth largest, said the Pakistani official closely involved in the decision on reducing the American presence.

On the American side, frustration has built over the Pakistani Army’s seeming inability to defeat a host of militant groups, including the Taliban and Al Qaeda, which have thrived in Pakistan’s tribal areas despite more than $1 billion in American assistance a year to the Pakistani military.

In a rare public rebuke, a White House report to Congress last week described the Pakistani efforts against the militants as disappointing.

At the time of his arrest, Mr. Davis was involved in a covert C.I.A. effort to penetrate one militant group, Lashkar-e-Taiba, which has ties to Pakistan’s military and intelligence establishment, has made deepening inroads in Afghanistan, and is perceived as a global threat.

The C.I.A. had demanded that Mr. Davis be freed immediately, on the grounds that he had diplomatic immunity. Instead, he was held for 47 days of detention and, the officials said, questioned for 14 days by ISI agents during his imprisonment in Lahore, infuriating American officials. He was finally freed after his victims’ families agreed to take some $2.3 million in compensation.

Another price, however, apparently is the list of reductions in American personnel demanded by General Kayani, according to the Pakistani and American officials. American officials said last year that the Pakistanis had allowed a maximum of 120 Special Operations troops in the country, most of them involved in training the paramilitary Frontier Corps in northwest Pakistan. The Americans had reached that quota, the Pakistani official said.

In addition to the withdrawal of all C.I.A. contractors, Pakistan is demanding the removal of C.I.A. operatives involved in “unilateral” assignments like Mr. Davis’s that the Pakistani intelligence agency did not know about, the Pakistani official said.

An American official, who spoke on the condition of anonymity, said without elaborating that the Pakistanis had asked “for more visibility into some things” — presumably the nature of C.I.A. covert operations in the country — “and that request is being talked about.”

General Kayani has also told the Obama administration that its expanded drone campaign has gotten out of control, a Pakistani official said. Given the reluctance or inability of the Pakistani military to root out Qaeda and Taliban militants from the tribal areas, American officials have turned more and more to drone strikes, drastically increasing the number of attacks in 2010.