IN STAND-UP comedy and politics, timing is critical. There was nothing “funny ha-ha’’ about the recent leak of US documents about the Afghanistan war implicating Pakistan and its Inter-Services Intelligence agency. But there was plenty of what the British call “funny peculiar’’ for sure.

The leaks followed a period of growing confidence of the ISI and Pakistan in their quest to work with Afghan President Hamid Karzai to rebuild relationships marked by severe historical distrust. How Afghanistan and Pakistan overcome the challenge posed by intelligence reports linking the ISI to hostile events in Afghanistan will determine Pakistan’s relations in the neighborhood and with the United States, as well as the trajectory of US withdrawal from the region. President Karzai’s press conference following the leak indicates that some damage has been done already to the nascent Pakistan-Afghan entente.

Until the leaks, recent high-level exchanges between Afghanistan and Pakistan resulted in a renewed commitment to security collaboration and trade relations, with a transit trade agreement signed under the watchful eye of Secretary of State Hillary Clinton. There was also the firing of two key members of the Afghan security establishment, who were seen as anti-Pakistan: interior minister Mohammad Hanif Atmar and head of the National Directorate of Security Amrullah Saleh.

Many analysts saw Karzai playing the Pakistan card in the face of a sudden US withdrawal. Pakistan saw this as an opportunity to reassert its comparative strength as a neighbor of Afghanistan, tying the two countries closer together for the first time in their fractious 62-year shared history and independent states. It also saw itself displacing India inside Afghanistan as a key ally.

Pakistan sees a pro-Pashtun stance as most useful and convenient in this strategy. After all, it has more Pashtuns than Afghanistan inside its own borders. But in doing so it risks alienating the non-Pashtuns as it did during and after the Soviet occupation. It also risks fueling internal ethnic division that will only lead to instability in Afghanistan. An unstable Afghanistan always has a contagion effect on neighboring Pakistan.

Now the flood of material unleashed by WikiLeaks has fed Pakistan’s insecurities and Afghanistan’s fears about the sanctuary available to the Taliban in Pakistan’s border regions. Pakistan is a country that has been stung so many times by bad relationships that historian Ayesha Jalal recently called it “paranoidistan.’’

Many in Pakistan suspect the recent leaks are a conspiracy to damage its budding relationship with Afghanistan and established aid links to the United States. It will take many a cool head in its civil and military hierarchy to ride out the storm that is building over the leaked information linking the ISI and retired ISI chief Lieutenant General Hamid Gul to the Taliban, which Pakistan is meant to be fighting on behalf of the United States.

The ISI has gone through many different purges in the past, but somehow the system fails to remove all the vestiges of the period when the agency held the lead position in the war against the Soviets in Afghanistan and had unfettered access to resources and power. Its senior ranks are routinely rotated. But field work may well be the weak spot when contractors are brought back to operate in border regions areas, such as the Federally Administered Tribal Areas abutting Afghanistan, where you need connections, memory, and experience.

Adding to the difficulty of severing those ties is the possibility that Pakistan continues to hedge in favor of Pashtun groups that it knows well against the possibility that the United States will depart sooner than expected from the region. Pakistan wants to ensure that it has a friendly group in power in Kabul. In recent weeks, it seemed it had plumped for President Hamid Karzai and he for Pakistan.

If they can ride out the storm unleashed by WikiLeaks, a stable relationship may emerge. If not, the final battle for Afghanistan may have begun sooner than expected, thanks to WikiLeaks.

Shuja Nawaz is director of the South Asia Center at the Atlantic Council. This article appears as an editorial in the Aug. 6 edition of The Boston Globe. Photo credit: Getty Images.