Today’s New York Times leads with an extraordinary article reporting that Ahmed Wali Karzai—the brother of Afghan president Hamid Karzai, suspected of being a significant player in that country’s lucrative drug trade—has been on the CIA payroll for much of the past eight years “for a variety of services, including helping to recruit an Afghan paramilitary force that operates at the C.I.A.’s direction.” (Karzai denies the allegation, and the CIA declined to comment.)

Reported by Dexter Filkins, Mark Mazzetti, and James Risen, and sourced to mostly unnamed “current and former American officials,” the story is a scoop that could have real consequences for how the war effort is perceived here—and help Americans understand how it’s seen by at least some sectors of the Afghan public. As the Times writes:

The ties to Mr. Karzai have created deep divisions within the Obama administration. The critics say the ties complicate America’s increasingly tense relationship with President Hamid Karzai, who has struggled to build sustained popularity among Afghans and has long been portrayed by the Taliban as an American puppet. The C.I.A.’s practices also suggest that the United States is not doing everything in its power to stamp out the lucrative Afghan drug trade, a major source of revenue for the Taliban.

More broadly, some American officials argue that the reliance on Ahmed Wali Karzai, the most powerful figure in a large area of southern Afghanistan where the Taliban insurgency is strongest, undermines the American push to develop an effective central government that can maintain law and order and eventually allow the United States to withdraw.

National-security commentators have begun to explore the story’s significance. At The Washington Independent, Spencer Ackerman writes:

At this point, everything about the U.S. policy toward the Afghan drug trade — from tolerance to eradication during the Bush administration to an evolving approach to cultivating alternatives — now ought to be questioned. As in questioned in open congressional session. CIA money funds a politically connected drug dealer. Opium funds the Taliban. We are in Afghanistan to fight the Taliban. How much CIA money has indirectly funded the Taliban?

In a follow-up post, Ackerman notes that the scoop should perhaps not be a surprise: America’s initial Afghanistan strategy, back in 2001, involved the CIA buying the support of warlords who made up the Northern Alliance. “But once you start paying warlords with dubious human rights records, it can be very difficult to cut off or phase out the payments, particularly when the political structure necessary to keep the Afghan governance enterprise that supports the U.S. presence in business is essentially held together with baling wire.”

The last point was echoed, in a way, from the other end of the ideological spectrum by Michael Rubin of the National Review. The CIA often has good reasons to work with bad people, Rubin writes. “The problem with the CIA, however — and I worry this is the case in Afghanistan — is when the desire to maintain the source leads the CIA organizationally to try to protect that source…there does not seem to be any check-and-balance within the CIA to force the institution and the case officers to see the forest through the trees, and to allow the downfall of sources when their power begins to erode the credibility or stability of a government.”

At his Abu Muqawama blog, Andrew Exum dissects what the CIA’s relationship with Karzai—which is all about counterterrorism—means for the military’s commitment to counterinsurgency:

…if this is true, and if the CIA is empowering Ahmed Wali Karzai at the same time in which NATO/ISAF [military forces] is saying abusive local power-brokers are a threat to mission success, then this is yet another example of NATO/ISAF carrying out one campaign in Afghanistan while the CIA carries out another — with both campaigns operating at cross purposes to one another…numerous military officials in southern Afghanistan with whom I have spoken identify AWK and his activities as the biggest problem they face — bigger than the lack of government services or even the Taliban.

(Counterinsurgency skeptic Matthew Yglesias, meanwhile, says that “this raises, in a very pointed way, the issue of whether COIN-in-practice stands any realistic chance of resembling the theory and rhetoric.”)

Exum makes clear that he has no independent knowledge about the CIA-Karzai relationship, but his reference to the views of “numerous military officials” supports the idea that the Times article is rooted in military sources. One of the few sources quoted by name is Maj. Gen. Michael T. Flynn, who does not tie Ahmed Wali Karzai and the CIA together (at least not on the record) but makes clear that the military has little use for the president’s brother. “The only way to clean up Chicago is to get rid of Capone,” he says. Another top military officer is quoted, anonymously, linking Karzai to the drug trade—something American officials have been reluctant to do publicly.

At Time’s Swampland blog, Joe Klein engages in some speculation about the story behind the story:

This has been in the wind for a while. And you’ve got to wonder why it has broken now, two weeks before the Afghan presidential runoff.

The most obvious conspiracy theory—and these are rarely right—is that the U.S. has decided to let this news slip now to adversely affect [Hamid] Karzai in the coming election.

A less obvious but, to my mind, more plausible theory is that the U.S. needed to make Ahmed Wali Karzai radioactive so that he could no longer run and ruin Kandahar province as its shadow governor.

Or, it may just be that the Times finally managed to nail a story that more than a few journalists had been pursuing.

Klein is right to dismiss the first theory—as frustrated as the U.S. is with Hamid Karzai, it’s not at all clear that his defeat would bolster the prospects for America’s mission. As for the others, it’s too early to say—it’s also not clear whether the story will make Ahmed Wali Karzai “radioactive” in Afghanistan, where it may not register as much of a surprise. In any case, in the coming days and weeks, it will be fascinating to learn more about this story—both how it came about, and its ultimate ramifications.

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Greg Marx is an associate editor at CJR. Follow him on Twitter @gregamarx.