The takedown of al-Qaeda leader Osama bin Laden in a Pakistani military town near that nation’s capital illustrates just how far U.S.-Pakistani relations have deteriorated.  It is time for America to recalibrate its relationship with Pakistan, which has significant implications for our success in Afghanistan.

Sunday, a U.S. Navy SEAL team acted on confirmed intelligence to covertly move on a fortress-like mansion in Abbottabad, Pakistan, to end an almost 10-year effort to capture or kill the mastermind of the September 11, 2001, attacks on America.  It took so long to bring bin Laden to justice because our so-called ally Pakistan hasn’t been sufficiently cooperative due to divergent interests in the strategically important Afghanistan War.

Pakistan wants to be the dominant player in a future Afghanistan to avoid having to defend both its eastern and western borders if India and Afghanistan become too close.  That explains Islamabad’s efforts to shape the Afghanistan endgame by pushing back—not cooperating—with Obama’s war strategy, such as by helping bring bin Laden to justice.

Last year Obama announced a strategy that surged 30,000 fresh troops into population centers to force out insurgents, establish governance, and train Afghan security forces.  The President promised to begin withdrawing troops this summer and turn over all security to a fully ready Kabul by 2014.

On top of his self-imposed time line, the President is also under pre-election pressure to show strategic success in the war—which has flagging support.  A recent Washington Post-ABC News survey found for the first time more Americans disapprove (49%) of Obama’s management of the war than approve (44%).

Obama admits, “Pakistan is central to our efforts to defeat al-Qaeda,” but that relationship has soured, undermining his strategy—the lack of cooperation regarding bin Laden illustrates the point.

That is why in part Obama recruited Army Gen. David Petraeus, commander in Afghanistan , to become director of the Central Intelligence Agency ( CIA ), the government’s primary agent engaging Pakistan.  Obama expects Petraeus, who rescued the war in Iraq and is reversing the trends in Afghanistan, to perform the same magic with the Pakistanis.  But Petraeus must first solve four daunting problems to win Pakistan’s cooperation if Obama’s strategy is to be salvaged.

First, Pakistan must stop supporting our enemy.  It is unbelievable Pakistani intelligence officials didn’t know about the location of bin Laden.  Likely, they played us for fools all these years to milk us for aid money.  Interestingly, that lack of cooperation was coming to a head even before the bin Laden operation.

Last week, Adm. Mike Mullen, chairman of the U.S. Joint Chiefs of Staff, said while in Islamabad that Pakistan’s Inter-Services Intelligence directorate (ISI) shelters fighters from the Haqqani network, a Taliban ally that has served as a Pakistani proxy.

Mullen said the ISI-Haqqani relationship was “at the core” of difficulties between the governments.  “It is the Haqqani network which is killing Americans across the border,” Mullen said.

The ISI’s substantial ties to the Taliban, al-Qaeda, and other right-wing Islamic extremists are common knowledge.  Last week, U.S. military documents obtained by WikiLeaks and reported by the New York Times identified the ISI along with numerous militant groups as allies of al-Qaeda and the Taliban.

Second, Pakistan must aggressively pursue al-Qaeda and the Taliban within its borders and deny them sanctuary.  Bin Laden left Afghanistan from his Tora Bora mountain hideout in late 2001 and has been hiding in that country.  It is hard to believe the ISI, which has enjoyed a long-term relationship with al-Qaeda, didn’t know his whereabouts.  But then again, Pakistan’s lack of aggressiveness against these enemies is an ongoing problem.

Last month the Obama administration reported to Congress that Pakistan lacks a “clear path toward defeating” the Islamic insurgency inside the country’s tribal region.  It noted Pakistani security forces repeatedly failed to keep militants from returning to areas cleared of the al-Qaeda-linked fighters.

Pakistan’s army has conducted several campaigns to suppress Taliban groups since 2001.  However, according to the administration’s quarterly report to Congress, the Pakistani army launched a major operation this January but “was failing for the third time in two years” to clear militants from Mohmand, one of the seven autonomous agencies comprising Pakistan’s tribal region, which borders Afghanistan.  The report states this is “a clear indicator of the inability of the Pakistani military and government to render cleared areas resistant to insurgent return.”

Third, Pakistan must support a full range of American covert actions.  U.S. counterterrorism strategy in Afghanistan relies on covert operations in Pakistan:  Agents monitor extremist groups planning actions in Afghanistan and American drones attack Taliban safe havens in northwest Pakistan.

Details regarding the bin Laden takedown will demonstrate whether Pakistan cooperated.  But the ongoing bitter dispute over covert CIA activities and drone attacks inside Pakistan is not in doubt and may explain why it took almost 10 years to get bin Laden.

Tensions over CIA activities peaked earlier this year when Pakistan arrested a CIA contractor after a shooting incident involving ISI agents.  That affair followed the withdrawal last December of the CIA station chief in Pakistan after his name was published by local media.

London’s Guardian reported in April that Pakistan has moved to expel hundreds of U.S. personnel, many believed to work for the CIA , by not renewing their visas.

Pakistani officials are also incensed by CIA drone attacks.  They complain the U.S. has stopped sharing intelligence on how it selects targets, according to the New York Times.  Islamabad claims it needs the information to eliminate collateral damage, but U.S. officials suspect the ISI is warning would-be targets.

Gen. Petraeus will have a difficult task repairing the ISI-CIA relationship.  “In its current form, the relationship is almost unworkable,” Dennis Blair, a former American director of national intelligence, told the New York Times.  “There has to be a major restructuring.  The ISI jams the CIA all it wants and pays no penalties.”

Finally, Pakistani officials must stop undermining America by pressuring Afghan officials.  The Wall Street Journal reported that Pakistani Prime Minister Yousaf Raza Gillani urged Afghan President Hamid Karzai to look to Pakistan and China for help instead of partnering with the U.S.

The Journal reported that Gillani made the statement during an April 16 meeting in Kabul with Karzai.  Gillani allegedly told Karzai the U.S. had failed Afghanistan and Pakistan, and that Karzai should not allow a long-term U.S. military presence in the country.  An Afghan official told the Journal, “There was a mention of China in the meeting, China as a country, as an emerging economic power, and that maybe we should reach out to a new global economic power.”

Dr. Abdullah Abdullah, a onetime Afghan presidential candidate and former foreign minister, told the Journal he had some knowledge of what was discussed at the Gillani-Karzai meeting.  “They said that the goals of the United States are confusing and uncertain, the American force is not reliable, and their power is not a reliable power,” Abdullah said.

Abdullah said Pakistan’s perspective on the U.S. is increasingly negative.  He opined, “One of the schools of thought in the Pakistani establishment is that the U.S. presence in Afghanistan is not for the stabilization of Afghanistan, but is for seizing Pakistan’s nuclear assets in due time.”

Solving these problems will be complicated for Gen. Petraeus, especially because Pakistani military leaders—the real power brokers in Islamabad—do not regard Petraeus as a friend.  Gen. Ashfaq Parvez Kayani, Pakistan’s army chief of staff, called Petraeus a political general, and has made little secret of his distaste for the man, according to the New York Times.

Petraeus’ chances of solving these problems are limited given Obama’s time line for withdrawal, America’s growing impatience with the war, and Islamabad’s compelling strategic interests to dominate Afghanistan’s end state.  Even a surge in aid on top of $18 billion already shoveled at Islamabad is unlikely to “force” Pakistan to reverse course.

America’s long-delayed operation to kill bin Laden illustrates the consequences of an uncooperative Pakistan.  Islamabad ’s same lack of cooperation is glaringly evident in the Afghanistan war.  Clearly, it is time America recalibrated its relationship with Pakistan and rethinks its Afghan strategy.