Rachel came to the same conclusion I did when first hearing about this story and trying to make some sense of it. Since it was public information that the CIA was going after al Qaeda terrorists, what made CIA Director Leon Panetta feel the need to come running to Congress as soon as he knew about this program, and to stop it immediately? Something isn't adding up here.

MADDOW: It has now been five full days since we first got news that the CIA had been operating some sort of secret program that it was actively hiding from the Congress. It‘s been three days since that allegation that the CIA was hiding that program at the direction of former Vice President Dick Cheney—in what would appear to be a direct violation of federal law.

Since the story broke, there has been lots of speculation about what the secret program was that Cheney didn‘t want Congress to know about. And while all the speculation is really titillating and makes for great headlines, it does seem—when you start to look more closely at it—that there‘s something not quite right here, at least something is yet unexplained.

Here‘s what we‘ve seen: “Newsweek” says, “CIA squads to track and kill al Qaeda terrorists.” “The Wall Street Journal” says, the program “was looking for ways to capture or kill al Qaeda chieftains.” “New York Times” says, “CIA Had Planned to Assassinate al Qaeda Leaders.” Liz Cheney, her own very special voice of America, described the program as “ways that we could capture or kill al Qaeda leaders.”

The reason that doesn‘t make sense is because this strategy of capturing and killing top leaders of al Qaeda, it‘s not exactly classified. It‘s not exactly a secret plan. That‘s the war on terror. That‘s the war on terror strategy we heard articulated again and again and again by the Bush administration.

(BEGIN VIDEO CLIP, MARCH 23, 2004)

GEORGE W. BUSH, FORMER PRESIDENT OF THE UNITED STATES: We have been chasing down al Qaeda ever since they attacked us. We‘ve captured or killed two-thirds of their known leaders.

Hundreds of Taliban and al Qaeda fighters have been captured or killed.

Two-thirds of known al Qaeda leaders have been captured or killed.

(END VIDEO CLIP)

MADDOW: Capturing or killing members of al Qaeda, it‘s not some secret operation. It‘s essentially the simplest construction of the whole idea of the war on terror.

So, this secretive “don‘t tell anyone” program that Leon Panetta shut down immediately upon learning of it last month had to be something other than just capturing and killing members of al Qaeda. Was it capturing or killing them in inconvenient countries, like countries that we are allies with?

Well, technically, Pakistan is our great ally in the war on terror, but we kill people there on a really regular basis. For example, June 23rd, “U.S. drone fires more missiles into Pakistan.” July 4th, “U.S. Drone attacks said to kill 17 at Taliban outposts in Pakistan.” July 8th, “U.S. Drone Attack Kills 12 in Northwest.”

How many times have you read headlines about drone attacks killing Pakistani civilians while we were targeting al Qaeda suspects in that country? If killing al Qaeda suspects inside the borders of our ally, Pakistan, doesn‘t even make the front section of the newspaper anymore, then a plan to kill al Qaeda suspects inside the borders of other countries hardly seems like something that would stop the presses in Washington the way that this program has and that would send the director of the CIA all but sprinting to Congress after calling the program off as soon as he heard about it.

Lawrence Wilkerson weighed in with his thoughts on why the program was kept from the Congress.

MADDOW: We‘ve heard all this speculation, all these leaks about what this program might have been. You were there in the first term of the Bush administration. Does any of this ring any bells in terms of what you knew about it at that time?

WILKERSON: It does ring some bells. We—very early on, after 9/11, at the State Department—learned from our ambassadors in the field that there were teams being dispatched to their cities, to their countries, and these teams were clandestine and they were essentially aimed at capturing al Qaeda leaders or al Qaeda affiliates and interrogating them and so forth.

So, the fact that it might have gravitated over to the CIA or the CIA might have joined in, which is something that happens a lot these days with Delta Force and other special operators is no surprise to me. But I take your same surprise—isn‘t that what we‘re supposed to be doing?

What I suspect has happened is what began to happen while I was still in the government, and that was we‘re killing the wrong people—and we‘re killing the wrong people in the wrong countries. And the countries are finding out about it, or at least there was a suspicion that the countries might find about it—find out about it, and so it was shut down. That‘s my strong suspicion.

MADDOW: When you, at the time, attempted to find out what was going on or at least to get answers to these ambassadors that you were hearing from around the world—how much were you able to find out about who these operators were, what their goals were, and who might have been—who might have been running that program?

WILKERSON: Well, at that time, Secretary Powell, of course, called Dr. Rice. She was the national security adviser and got virtually nowhere, and so, he wound up calling Secretary Rumsfeld. And after some hemming and hawing—which was Rumsfeld‘s forte—he finally admitted that he had dispatched some of these teams.

I don‘t think we ever got a handle on every place he dispatched them. I think he‘d sent them to the Horn of Africa, to Maghreb. He‘d probably sent them to Afghanistan and Pakistan. He probably sent them to Indonesia, Southeast Asia in general, and he was after everyone from Abu Sayyaf to al Qaeda. As Doug Feith points out in his book, “War and Decisions,” they were taking on every terrorist they could get their hands on.

So, I don‘t think, at State, we ever knew the full range of his deployments. And in most cases, I think it was Delta Force. It was probably weren‘t directly through the Special Operations Command commander in Tampa, didn‘t go through the combatant regional commanders. In other words, they didn‘t even know it was happening either.

They didn‘t go through the ambassadors; didn‘t even go through the CIA station chief, until later when I believe the CIA became involved in it. And then, of course, it became both a military and an intelligence agency operation.

MADDOW: The whole reason that this has turned into a huge story is because of the claims from people with knowledge of what happened inside those intelligence committee meetings at the end of June that Leon Panetta came in and said, “I didn‘t know about this program until 4 ½ months into my tenure at the CIA. It is now over and it was kept from Congress covertly on direct orders from Vice President Cheney.”

We are told that that‘s what Leon Panetta said. And so, there is a degree of hearsay here. But it seems to be confirmed by multiple sources.

If this is something where we‘re talking about Delta Force operators, we‘re talking about military personnel doing this sort of thing, how does it fit in that Dick Cheney would be ordering the CIA not to tell Congress about it? That‘s the part I don‘t get.

WILKERSON: Well, I think that‘s pretty clear. If you know the history of the CIA, you know that presidents have told the CIA to do things since 1947 that the CIA then lied to Congress about. It‘s laughable that the CIA has never lied to Congress. They lie to Congress on a routine basis. It‘s part of their portfolio.

However, it‘s usually the president—in fact, I won‘t say usually—it‘s always been the president who directs the CIA to do these things and then takes the fall if—like Eisenhower sending U2s over the Soviet Union, suddenly Gary Powers is shut down and Eisenhower‘s plans and his activities are revealed and he has to take the blame for it. This is unprecedented.

Now, we have a vice president who has apparently authorized these activities—whether or not the president knew or not is anyone‘s question. I don‘t think he probably did. The division of labor in the White House in that first term was Cheney gets everything that‘s important and I get everything that‘s easy, if I am Bush.

So, Cheney was making most of the national security decisions, most of the domestic decisions that mattered, and he was certainly making most of the decisions that involved lethal action in the war on terror.

MADDOW: And the inclination of Mr. Cheney, as we know, is towards secrecy. That might explain why he felt it had to be overtly kept from Congress?

WILKERSON: Absolutely. And that‘s not an uncommon thing, either, as I said. But it‘s the president that normally directs and it the president who takes the fall.

MADDOW: I suppose it‘s immaterial that in 1974, President Ford issued that executive order banning assassinations by the CIA. But, you know.

WILKERSON: I‘m sorry; but predators have been assassinating people under CIA and military guise for some time now.

MADDOW: It‘s always both good and tremendously alarming to talk to you.

Retired Army Colonel Lawrence Wilkerson, chief of staff to Secretary of State Colin Powell during the first term of the Bush administration—thank you so much for your time tonight, sir.

WILKERSON: Thank you, Rachel.