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An official story is forming about the secret program that the C.I.A. hid from Congress: the agency planned to organize assassination squads to target Al Qaeda terrorists around the world, according to a lead article in today’s New York Times.

Although this account has gained widespread acceptance, there’s reason to be skeptical. As I noted recently in an update, the Washington Post reported that the program “was not a covert action” and concerned “a intelligence-collection activity run by the CIA’s Counterterrorism Center.”

In this light, consider the following post from Time magazine’s Swampland blog (emphasis added):

But two former ranking CIA officials have told TIME that there’s another equally plausible possibility: The program could have required the Agency to spy on Americans. Domestic surveillance is outside the CIA’s purview -– it’s usually the FBI’s job – and it’s easy to see why Cheney would have wanted to keep it from Congress.

Both officials say they were never told what was in the program, and that they’re only making calculated guesses. But their theory gibes with other reports, quoting ex-CIA officials, that say the program had to do with intelligence collection, not assassinations.

“People may want this to be about hit squads bumping off shady Saudis in Geneva, but that’s very unlikely,” says one official. “More likely, it was a plan to spy on some suspicious American citizens or organizations, without telling the FBI.”

The correct answer to the mystery, as this Swampland post rightly acknowledges, must account for former Vice President Dick Cheney’s order that the C.I.A. not inform Congress about the program. Why would Cheney make such a demand about an assassination program that targeted enemies against whom the U.S. was at war, that was similar to the drone attacks the military openly uses, and that was not even operational? Could Cheney expect the program to cause such uproar that he was wiling to risk breaking the law in not briefing Congress?

Even supposing the “C.I.A. hit squad” story is true, questions remain. Why did the C.I.A. assassination program remain at the planning stage? Was it because the White House decided to pass responsibility instead to the Joint Special Operations Command (JSOC), the military special operations unit that, according to Seymour Hersh, ran an “executive assassination ring” that reported to Cheney and had no congressional oversight? For much of time in question, JSOC was run by Gen. Stanley McChrystal, who is currently heading our efforts in Afghanistan. Are we conducting assassinations there today? And if we are, does Congress approve? Why isn’t it prone to the same grossly immoral conduct as previous covert assassination programs?

Whatever the answers to these questions, there can be no doubt that the American people deserve a full investigation.

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