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This is a RUSH transcript from "The O'Reilly Factor," January 6, 2014. This copy may not be in its final form and may be updated.

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"Back of the Book" segment tonight, very bad things happening in Iraq, Syria, and other parts of the Middle East. You may remember that President Obama said that al-Qaeda was on the roves.

But al-Qaeda has now reconstituted itself in Iraq and a civil war may break out there. Joining us from Washington with some advice for the president, Charles Krauthammer. So, what would you tell Mr. Obama to do right now in Iraq.

CHARLES KRAUTHAMMER, FOX NEWS CONTRIBUTOR: Well, his options are all extremely bad. And the reason is that he made a terrible decision to pull out in 2011.

I mean, why are we negotiating right now in Afghanistan in agreement to leave behind a residual force, so we can arm and train the Afghans, so we can have a base of operation for Intelligence, so we have a base for special odds, and so that we can moderate and mediate in the government and between the government and its opponents --

O'REILLY: Let me play devil's advocate.

KRAUTHAMMER: -- which is what we should have done.

O'REILLY: OK, but let me play devil's advocate.

KRAUTHAMMER: What we should be doing in Iraq.

O'REILLY: What we were told -- and, both sides, Democrats and Republicans did acknowledge this -- was that Maliki, the leader of Iraq, would not indemnify U.S. forces against prosecution there.

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And that Joe Biden, as you know, who was trying to do this negotiation, --

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-- leader of central force, couldn't because any U.S. Military person charged with a crime are going to be put into the Iraqi system, which is insane.

And they wouldn't bend on it. And that's why we didn't leave residual force. Does that have any validity.

KRAUTHAMMER: No, that story is rubbish. That's a cover story for the fact that Obama proposed a reasonable small number of residual Americans who would stay behind, about 3,000 which would be useless.

All their time would be spent protecting themselves, like the force that we had in Beirut, tragically, in the early 80s. Instead of speaking about a number that would have been serious, $10 or $20,000 which Archimedes had recommended. The Iraqis understood that we weren't serious.

O'REILLY: OK. So, you just think that that's a canard, they just threw it out, --

KRAUTHAMMER: It is, it is a canard.

O'REILLY: -- that the president wanted to get out of there with everything. But didn't his advisors, -- and, certainly, you said and I said it -- if you do this, this is what the result is going to be. And, now, we're seeing that our prophecies --

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-- are coming true.

KRAUTHAMMER: Yes.

O'REILLY: Mr. Obama certainly had to know that that was possible.

KRAUTHAMMER: Look, I don't know what he knew. But I knew it, you knew it, others said it was absolutely obvious. And, most interesting of all, The New York Times, which is not exactly a right-wing rag, had a front-page article just yesterday, saying it is the vacuum created by Obama, by the United States in leaving nothing behind --

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-- nothing behind, that has invited in al-Qaeda and created the resurgence. Remember, Iraq has no air force. One of the duties would have been for the U.S. to stay, to train, and to construct a new air force.

Instead, Iraqi air space is controlled by whom, by Iran, instead of us. We have no base of operations for Intelligence. We have no way to do counterinsurgency.

The war was won. The al-Qaeda was defeated. And the worst part about it is we would have had influence on Maliki as we did when we were there, as a way to moderate a sectarianism, as a way to work with the Sunnis, what he did at the end of the --

O'REILLY: Yes, we must tell the audience that one of the reasons for this civil war is that Maliki in Baghdad is treating the Sunnis poorly, so the Sunnis are now allying with al-Qaeda. And, thus, we have all that chaos. OK.

KRAUTHAMMER: And that, in part, is because when we left, Iran stepped in as the leading power in Iraq. And it was its pressure on Maliki we use to go after the Sunnis.

O'REILLY: OK. So, now, where is all this going to lead. So, I think there could be -- I don't see the Iraqi Armed Forces being able to throw al-Qaeda out at this point.

So, al-Qaeda builds its strength in the center of the northern part of the nation, Iraq. And then al-Qaeda goes into Syria, and causes all trouble in Lebanon, everything. So, right, that's what it's going to be.

KRAUTHAMMER: Well, al-Qaeda is already in Syria. And the border between Iraq and Syria has been effectively erased.

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What we have to do now, -- and this is tragic -- instead of using our bases and the forces we had in Iraq, we're going to have to reconstruct something like that in Jordan, which will be the next to go.

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Jordan, right now, is looking at a frontier with Iraq. And Syria dominated via al-Qaeda, and it will be the target. So, we're now going to have to redo, reinvent the wheel, and to establish a defensive presence in Jordan as a result of the evacuation of Iraq.

And we are now two years late, three years late. But we're going to have to increase and actually start supporting the rebels in Syria who are not Islamists.

We are already late on that but that's our only hope -- Jordan on the one hand, and the non-Islamist --

O'REILLY: What a mess, huh.

KRAUTHAMMER: -- rebels in Syria on the other. And it is a mess.

O'REILLY: What a mess.

KRAUTHAMMER: And the reason at the root is the evacuation that Obama ordered.

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