The ex-Bush aide appeared to promote his new book Courting Disaster , which defends and advocates for the administration's CIA's interrogation program. After Thiessen argued that the tactics stopped another terror attack in the U.S. after 9/11, Stewart lectured, "The bombings in Britain, the bombings in Afghanistan, the bombings in a Iraq. It's a selective world that you live in and you must be lovely to live there. Things are not so clear cut."
At the end of the segment, Stewart started to go to break and added, "We'll go to commercial and then we'll keep talking." An incredulous Thiessen retorted, "So, you talk and we go to commercial?" He challenged, "I can't get my points on the air?" A sarcastic Stewart quipped, "Geez, I'm trying to think of a way can I remove what I said and just have you speak." He then offered Thiessen a chance for rebuttal on the internet.
This did happen, but very few people are actually going to go to Comedy Central's website and listen to the extended  segments .
(Thanks to Ben Graham for transcribing the segment.)
A partial transcript of the March 9 segment follows:
JON STEWART: Let me get to the larger point here which I think is maybe the issue. The thing that I object to is the idea of safety. And I'll explain that. The idea that that can be a concrete certainty. This makes us safe. This doesn't. These are subjective realities. The idea of something that makes us safe, you can make the argument that Guantanamo keeps us safe because there are bad people in it. They can make the argument that by having Guantanamo open it allows easier recruitment for terrorists, which ultimately--Scott Whitlock is a news analyst for the Media Research Center. Click here  to follow him on Twitter.
MARC THIESSEN: I disagree with that entirely.
STEWART: I know you disagree with it, but I'm saying that is a valid argument.
THIESSEN: Well, I don't think it is. There was no Guantanamo Bay when they tried to blow up the World Trade Center in 1993.
STEWART: It's not the only reason but it all goes into- What I'm saying is-
THIESSEN: Let me make my point-
STEWART: Let me just very quickly go. [Thiessen laughs in frustration.] It's a- As conservatives would like to say it's a complex adaptive system very similar to climate change.
THIESSEN: Except it's real. [Laughs.]
STEWART: And Republicans and conservatives are suggesting without any of the science that backs climate change that they know the equation, that they can solve the unsolvable, that Liz Cheney knows more about this than say Matthew Alexander who was doing the interrogating.
THIESSEN: Matthew Alexander interrogated people for three months. The people that -
STEWART: How long did Liz Cheney do it for?
THIESSEN: The interrogators that I talked about in this book, where you meet the interrogators who-
STEWART: Not all of them, the ones that you chose.
THIESSEN: The ones that-
STEWART: Not all of them.
THIESSEN: The ones that ran the program.
STEWART: Ali Soufan is not in this book.
THIESSEN: Actually he is in the book.
STEWART: Well, he wouldn't talk to you in the book.
THIESSEN: He wouldn't talk to me, but I talked about him.
STEWART: Oh, I know.
THIESSEN: Ali Soufan, the sainted hero of left who says we can get all this information.
STEWART: [interrupting] Sorry, sorry.
THIESSEN: I appreciate the enthusiasm. Ali Soufan the sainted hero of left who says we can get all this information with the FBI's techniques. He was put in charge of the interrogation of Muhammad Al Qahtani, the 20th hijacker in Guantanamo Bay and got nothing from him. Ali Soufan then threw him into the navy brig for two months. Told them that he could have no human contact, people had to wear masks. This is in the department of Justice report and got nothing still. It was only when the military took over his interrogation that they got interrogation reports out of him. Ali Soufan failed with his techniques to break. And on top of that Muhammad Al Qahtani said the worst thing that happened to him in Guantanamo Bay was Ali Soufan putting him in two months in isolation. This is not so clean.
STEWART: Absolutely. I think the point is that it's not clean. You can't know for certain.
THIESSEN: No you can't.
STEWART: And when these things.
STEWART: Yeah, sorry.
THIESSEN: Jon, when Khalid Sheikh Mohammed was brought into CIA custody he had information about terrorist attacks planned on the united states. We were not attacked for seven years after the 9/11 attacks. So there's a reason for it.
STEWART: We were not attacked for seven years after the first World Trade Center- on our homeland.
THIESSEN: Not on our home land. They blew up the World Trade Center, the bombings in east Africa, the USS Cole, then finally 9/11.
STEWART: The bombings in Britain, the bombings in Afghanistan, the bombings in a Iraq. It's a selective world that you live in and you must be lovely to live there. Things are not so clear cut. And the idea that you can state equivocally that these lawyers- Let me say this quickly. We'll go to commercial and then we'll keep talking.
THIESSEN: [Laughes wryly] So you talk and we go to commercial?
STEWART: That's right. Honestly when I come on your show I'd be delighted you to let you do that. But, the idea that you can castigate people as though they are purposefully making America less safe and in league with the terrorists that we're fighting because they disagree with your ideas about safety, I think what is offensive about that. We can talk about. It won't be on the show. It will be on the internet unedited.
THIESSEN: I can't get my points out on the air?
STEWART: I thought-
THIESSEN: You did most of the talking.
STEWART: I apologize then. I will let you- Geez, I'm trying to think of a way can I remove what I said and just have you speak. Honestly you feel like you I've not let you make any points.
THIESSEN: I think you talked right through me.
STEWART: I sincerely apologize. We will. We will come back. You can correct it on the web and people will judge how poorly you've been treated. I do apologize. It's techniques I learned.