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Is the White House purposely manipulating intelligence?

This is a rush transcript from "Special Report," November 26, 2015. This copy may not be in its final form and may be updated.

(BEGIN VIDEO CLIP)

BARACK OBAMA, PRESIDENT OF THE UNITED STATES: I don't know what we'll discover with respect to what was going on with Cent Com. I don't know the details of this. What I do know is my expectation, which is the highest fidelity to facts, data, the truth.

LT. GEN. MICHAEL FLYNN, RET, FORMER DEFENSE INTELLIGENCE AGENCY DIRECTOR:
The focus of this investigation ought to start right at the top. Where intelligence starts and stops is at the White House. The president sets the priorities, and he's the number one customer. If he's not getting the intelligence that he needs, and if he's not paying attention to what else is going on, then something else is wrong.

(END VIDEO CLIP)

DOUG MCKELWAY, ‘SPECIAL REPORT,’ HOST: We've known for some time that there have been rumors and indeed significant pieces of intelligence that when the president called ISIS the jayvee team he was being perhaps disingenuous and ignoring what his intelligence were providing the National Security Council. In fact as early as last September "The Daily Beast" reported, and I quote, "More than
50 intelligence analysts working out of the U.S. military Central Command have formally complained that their reports on ISIS and Al Qaeda's branch in Syria were being inappropriately altered by senior officials."

And now thanks to Steve Hayes at "The Weekly Standard" who put a piece online last night at "The Weekly Standard" website, there is much more to the story. Steve has connected the dots, and they point in large part to the White House. Let's bring in our panel, Steve Hayes, senior writer for "The Weekly Standard," Tom Rogan, columnist for "National Review," and syndicated columnist Charles Krauthammer. Steve, let's get to you.

STEVE HAYES, SENIOR WRITER, "THE WEEKLY STANDARD": This has, I think, been one of the big questions is how much of this comes from the White House. The story that people have focused on over the past several months deals with ISIS manipulation or alleged manipulation at Central Command in Tampa, Florida. And the question is why were these senior advisors, senior analysts changing reporting from younger analysts, more junior analysts, and sending it on to the White House, reporting that sort of fed into the White House narrative of making progress against ISIS?

And it's an ongoing investigation. It's an important investigation. But I would argue that it's a side investigation. And, really, it's part of a much longer story and one that certainly we've talked about here before that goes back to the White House and the National Security Council and others in the administration shaping intelligence, in some cases denying access to intelligence, that deals with Al Qaeda.

And the example that we give in this story is the National Security Council basically turning down Defense Intelligence Agency analysts who wanted to have a full look at the Usama bin Laden documents. They were told repeatedly that they couldn't see the whole collection. Then finally they were granted access by the CIA director, but James Clapper, by the Defense Intelligence Agency director, and the National Security Council stepped in and denied them that access and in effect shut down the analysis and examination of these bin Laden documents. We have a DIA analyst Michael Pregent who says on the record the National Security Council stepped in and denied us access to these documents.

MCKELWAY: He's one of three sources, main sources that you cite. And I think that's what makes this so unusual. In fact the documents that were obtained during the raid on bin Laden were described as voluminous, enough to fill a small college library. And many of those documents we still have not seen.

HAYES: Virtually all of those documents we still have not seen. We've seen about 130 of them thus far. So there are literally more than a million that haven't been declassified and released.

MCKELWAY: Where does this lead?

TOM ROGAN, NATIONAL REVIEW: I think Steve has obviously done the reporting on this. But I think what it shows in the context of previous situations -
- you can go back. It's not just about the Islamic State, but also, for example, Iran. You look at the 2011 plot to blow up the Saudi foreign minister in D.C., and all of this, I think, takes it centering in a negative way in how the NSC process, the National Security Council process, is run by Susan Rice down. I think it would be very challenging to find a military career officer or an intelligence official who has good things to say about how that process works. Of course, intelligence is one side. But intelligence leading to the envelope of the commander in chief develops policy.

MCKELWAY: So there are some indications that Congress is very much interested in looking into this. Here is Senator Dan Coats of the Senate Intelligence Committee.

(BEGIN VIDEO CLIP)

SEN. DAN COATS, R, INDIANA: So we have to get to the bottom of this. But we also have to look at whether or not the White House has sent signals out basically saying, well, really, we don't assess it as bad as you do, and are you sure, you're right, and maybe causing some people to maybe make some adjustments to justify their decision making.

(END VIDEO CLIP)

MCKELWAY: He makes a good point Charles, that intelligence is only one piece of the puzzle. You can go back to criticizing intelligence as far as back the Vietnam War, perhaps much earlier than that. You look at the situation with George Tenet during the Bush administration where he said the fact that Saddam Hussein had weapons of mass destruction was a, quote, "slam dunk."

CHARLES KRAUTHAMMER, SYNDICATED COLUMNIST: Well, in the Iraq case, it's a hell of a coincidence that every other intelligence agency in the world, the Germans, the French, the British, the Israelis, who had a high interest in this, concurred with Saddam having the weapons of mass destruction.

But in this particular case with Obama, he sent out the signal from the first weeks he was in the White House, when he abolished the term "The War on Terror" and then his theme in his reelection campaign, and this is what I think sort of trapped him into this status where he is now in denying as much as he can deny. The theme of the 2012 campaign was the tide of war is receding. Al Qaeda is on the run and has been decimated. And he ran on that, and there was a lot of evidence that they tried to make that case.
That's why with the Benghazi they had to invent the video because otherwise the truth contradicted this idea. And that carried him into his reelection.

Now he's sort of stuck with that. I don't really know whether he truly believes, for example, that ISIS is less of a threat than just about everybody in the world thinks or whether he's being cynical about this.
It's not a good choice. He's either delusional or cynical. I'm not sure which to choose. The benign explanation is that he got trapped into this running into 2012, and he is stuck with the narrative that the tide of war is receding. And he keeps trying to insist on that as we saw in the press conference he had over in Turkey, which was a disaster. And I think that's really where he is, a state of denial, but quite cynically doing it because he knows that his claim to fame, his foreign policy achievements such as it is was going to be ending the tide of war and suppressing and decimating the terrorists.

MCKELWAY: Steve, go ahead.

HAYES: Just to pick up on what Charles is saying. Michael Flynn, the former director of the Defense Intelligence Agency, somebody who has worked at the highest levels of the U.S. intelligence community really for several decades, but especially in the past 10 years, said the other night on Megyn Kelly's show the president effectively misled the country in the lead up to the 2012 presidential election. And Flynn says at the time he was providing intelligence to the president, to the White House that was included in the presidential daily brief that said that Al Qaeda had doubled in strength. The president was running out and telling the American people that Al Qaeda had been decimated.

And to Tom's point about Iran, I have three in this article and a previous article, have three senior DIA officials on the record saying that we have a lot to learn about Iran's role with respect to supporting Al Qaeda that's in these bin Laden documents but has not been released. And their view is the administration is preventing its release because the administration was hell bent on the nuclear deal.

MCKELWAY: A quick question to you, at the time the CIA was sitting on this treasure-trove of Usama bin Laden documents, who was the director at the CIA?

HAYES: David Petraeus. He was basically on two sides of the dispute. Early he was in favor of allowing Cent Com and the DIA team access to these documents because they're the ones providing intelligence to the war fighters. But at some point along the line he flipped. Late spring, early summer of 2012, he flipped and no longer wanted these -- this other team to have access to this.

MCKELWAY: Let me interject. Was that at the time when rumors were surfacing that he was having an affair?

HAYES: The official story is he didn't find out and nobody found out until the fall. And of course he wasn't let go from the CIA until after the election. So we don't know about that. But, you know, there are people certainly who have raised those questions.

MCKELWAY: Next up, who gets to decide whether Syrian refugees come into your neighborhood?

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