Just when the relationship between the United States and Pakistan seemingly could not get more strained, it has. Links between Islamabad and Washington are fraying at an accelerating rate in the aftermath of the successful Navy SEAL raid on Abbottabad. This secret alliance, a cornerstone of U.S. counterterrorism policies for many years, is entering uncharted waters and may be sinking altogether.

Last weekend, still shaken by the death of Osama bin Laden in a Pakistani garrison town within sight of the country’s military academy, the Pakistani media reported the name of the CIA Chief of Station in Islamabad. This unconcealed act of revenge by the Inter-Services Intelligence Directorate, America’s ostensible partners, took direct aim at Washington. Last December, the previous COS had to be evacuated from Islamabad when his name appeared in the local media. Given that the COS’s identity is declared to a small number of Pakistani officials, the message from Islamabad in recent months has been difficult to miss.

This sort of spy-war has high stakes, as U.S. intelligence personnel have been killed in Pakistan in recent years. Old hands recall the murder of Richard Welch, COS Athens, in 1975, after his identity was revealed in a KGB-linked magazine. Comments from Pakistani officials that the current leak is no big deal because almost no one knows what the COS looks like are less than reassuring and indicative of a mindset that brings the entire relationship between the ISI and U.S. intelligence into question.

To say that relationship has long been complicated is to exercise considerable understatement. Whatever the ISI has done against al-Qaeda—and even the deepest skeptics about Pakistani motives do not deny that the ISI has at times been very helpful—the realization that Islamabad is a frenemy in the struggle against Islamist terrorism is causing consternation in Washington, as it should.

In truth, this reassessment is overdue, and has been delayed only by institutionalized denial, not to say escapism. While the ISI’s cooperation has been vital to our al-Qaeda operations in South Asia since 9/11, it has also complicated matters at many levels. The lack of Pakistani civilian control of the military generally, and the ISI specifically, should no longer constitute a pass for dubious conduct. The unspoken quid pro quo—that the U.S. and other Western partners would look the other way on certain ISI misdeeds, especially its support for “liberation movements” in Kashmir and Afghanistan as long as it worked with us against al-Qaeda—has been overtaken by events in Abbottabad and elsewhere.

This alleged wall between acceptable and unacceptable jihads has existed only in the Western mind anyway. The case of David Headley ought to have caused a fundamental reassessment, yet did not. Born Daood Gilani, this Pakistani-American drug dealer-cum-jihadist played a key role in the 2008 Mumbai attacks executed by Lashkar-e-Taiba, one of the ISI’s in-house terrorist groups. Headley spent several stints in LeT training camps, witnessing the close ties between Pakistani intelligence and the jihadists, and performed pre-attack surveillance for the Mumbai operation, a brutal spectacular that killed over one hundred and fifty civilians (four of them Americans) and wounded twice that number. Headley, who was working as a DEA informant, has provided critical first-person testimony about ISI involvement in Islamist terrorism, including the role of Pakistani senior officers in funding the Mumbai attack, among others.

The ramifications of the Headley case have been one of the causes of the fraying of ties between Islamabad and Washington. Even more provocative, from the Pakistani viewpoint, has been the increasing number of U.S. intelligence operations run without coordination with the ISI, known as “unilaterals” in the trade. While it is hardly unknown for the CIA and other agencies to run unilaterals, especially against high-value targets, even in friendly countries, this has grated on Islamabad, which appears fearful of what our personnel might find if they start digging too deeply. Pushback culminated in early 2011 with the arrest of Ray Davis, a CIA contractor, who shot two armed Pakistanis—suspected intelligence operatives—whom Davis believed threatened him. Davis was released after payment of bloodmoney to the families, but this public spectacle brought the always-touchy relationship between Islamabad and Washington to a new low.

They have descended further still with the outrage in Pakistan over the Abbottabad raid, the ultimate unilateral. The embarrassment of the Zardari government, which has had trouble knowing quite what to say to the global media, has been matched by the fury of the ISI, now that it is obvious to all that they were either sheltering bin Laden or were so incompetent as to have had no idea the world’s most wanted man was living, barely concealed, practically in a Pakistani Army base.

For the first time, serious pressure is mounting in Congress to investigate our relationship with Pakistan and get to the bottom of exactly what the ISI is up to. While administration officials have counseled caution, it is difficult to see how tough questions can be avoided now that the American public has gotten an indelible suggestion of deep Pakistani duplicity. Certainly the time has come to examine the real agenda of the tough-minded and inscrutable ISI, known as “the Black Snake” to the Taliban, who often doubt their motives as much as Americans do.

What happens now? For years, Islamabad has gotten away with a great deal, reckoning that the U.S. needs Pakistan’s cooperation against terrorism more than Pakistan needs American largesse. However, given the lamentable condition of Pakistan’s economy, which is heavily dependent on U.S. aid, that equation may no longer look the same. The mounting global perception of Pakistan as a rogue state hardly helps Islamabad’s case.

As al-Qaeda searches for a new leader, one of the candidates is reported to be Ilyas Kashmiri, a Pakistani jihadist with a low public profile but much operational experience, including plans to attack the United States directly. Kashmiri has been waging holy war since the 1980s and has a long relationship with the ISI, reportedly dating to the struggle against the Soviets in Afghanistan. He faces indictment in the U.S. for his close links to David Headley. While it is unlikely that al-Qaeda, whose leadership to date has been heavily Saudi and Egyptian, would want a Pakistani to take over, Kashmiri’s extensive experience would undeniably help keep the global jihad going. If a terrorist with such close ties to the ISI takes over al-Qaeda, some long-deferred questions about the relationship between Pakistan’s “deep state” and Islamist terrorism will have to be answered by Washington.