This is a rush transcript from "On the Record," November 25, 2009. This copy may not be in its final form and may be updated.

GRETA VAN SUSTEREN, FOX NEWS HOST: Well, like it or not, they are coming here. Five 9/11 co-conspirators, including Khalid Shaikh Mohammed, are coming to New York City for a trial in a federal civilian court. Opposition is loud and fierce.

Former U.S. ambassador to the United Nations John Bolton joins us live. Good evening, Ambassador. And Ambassador, you're not wild about this idea, are you, sir.

JOHN BOLTON, FORMER U.S. AMBASSADOR TO THE U.N.: No, I think it's a major strategic mistake by the administration. I think it reflects a pre- 9/11 mentality that you can treat terrorism like it's a law enforcement matter, rather than what it is, a war on the country. And I think the signal that it sends to the terrorists overseas is very, very dangerous for the country down the road.

VAN SUSTEREN: Well, there are a couple of issues that I see. One is why a civilian court and not a military? And even if -- you know, even if it had -- even if the person makes the decision that it should be in a civilian federal court -- of course, is Eric Holder here, the attorney general is -- why New York City? Why not Montana or Gitmo, much like they did in the Oklahoma City bombing case was tried in Denver? You know, why New York?

BOLTON: Well, I think on the first question, it really -- there's a lot more than just, Do you try them in a civilian court, or do you try them in a military court? In the first place, as a -- as a matter of looking at it through the war paradigm, the first thing you want to do capturing somebody like Khalid Shaikh Mohammed or many of these other people at Guantanamo is not worry about the trial for the terrorist acts they've committed but getting information from them that we can use in the continuing war. And I think the trial is really almost secondary to the larger strategic objectives.

In terms of putting it in New York, you know, it is -- it -- one of the reasons it's attractive to Khalid Shaikh Mohammed is it's the center of media attention for him to make his case to the world. He's not a traditional defendant. He's not trying to prove his innocence. He's not trying to get an acquittal from the jury. He's there, as his lawyer has already said, to conduct a show trial. And I think the risk is it will draw other terrorists to New York to make their point, as well.

VAN SUSTEREN: And of course, you made the comment you wouldn't bring your family there during the trial or something. I don't know if I read that wrong, but...

BOLTON: Well, my -- my -- my daughter lives and works in New York, and I don't expect she'll pay any attention to that. But my point was that you are endangering innocent people's lives unnecessarily. I don't think there's any question the risk of terrorist attack goes up. We all hope federal, state and local authorities will be able to defend against it, but why give the terrorists the opportunity to begin with?

VAN SUSTEREN: Well, taking it one step further to the whole issue of the trial, with the recognition that, you know, that's a decision that has been made and it's going to happen, the thing that strikes me is that guilty people are found not guilty every single day of the week. Not guilty people are convicted every day -- every day of the week, so it's an -- it's our best system we can do, but it's imperfect. We've got a guy who was waterboarded 183 times. The attorney general himself has testified that he says that's torture, so it's unlike anything that comes out there could be used against him. So the whole trial procedure is -- is at high risk, from the prosecution standpoint. Even though Attorney General Holder says, you know, that he's got a strong case, there is a risk.

BOLTON: Look, Greta, I was a litigator, like you were, for many years, and you know, you can prepare as hard as you want for a trial. I never went into any trial absolutely convinced what the outcome was going to be. And I think the points you've made show why the law enforcement paradigm simply doesn't work here. A terrorist in this context is not just a bank robber on steroids. And the circumstances under which Khalid Shaikh Mohammed was apprehended, much of the evidence gathered, isn't in the context of a civil, constitutional society where you can have appropriate due process for criminal defendants.

In a war, you don't have police tape marking off crime scenes. You don't have infantry soldiers carrying little glassine bags to put evidence in. People don't get Miranda warnings because it's not a criminal environment.

VAN SUSTEREN: But I -- I don't -- I have never tried a case in a criminal -- I mean, in a military forum, but people who work within the military framework have an enormous amount of respect. I've seen juries where I never thought in a million years someone would be found not guilty because the jury's made up of the military people. So is there something fundamentally wrong in terms of -- of these military panels? Is -- you know, what's wrong -- why -- why not put them there? What's the argument against putting them there?

BOLTON: Well, ultimately, I don't have any trouble when you have somebody who commits an act of terrorism like this, but I don't think it's an issue that you want to rush them into trial in a military tribunal. I want to make sure...

VAN SUSTEREN: But in any tribunal -- I mean, I -- do you just want to hold them indefinitely or do you want to give them some sort of, you know, finality that we should, you know, figure out what to do with these people?

BOLTON: Well, I'd hold them indefinitely in any case. I mean, even if you believe in the Geneva convention's applicability, which -- which is incorrect, but even if you did, you hold prisoners of war for the duration of the conflict, and I think this conflict is going to go on for a long time. The fact is military tribunals do give a considerable amount of justice. They are not show trials. The show trial we're going to see here is going to be put on by the defense.

VAN SUSTEREN: What I don't understand, though, is if -- I mean, if we -- if the government insists on putting them on trial in a federal civilian -- a civil trial -- or a civilian trial, why not just send the judge down to Gitmo and do that there instead of bringing the whole the show and all the expense up to New York and all the risk to New York? Is there anything to stop them from moving the judge to the trial?

BOLTON: Well, I think you've got a jury problem, although, you know, you've got another...

VAN SUSTEREN: They're going to be sequestered anyway. They're going to be sequestered anyway, so sequester them at Gitmo. I mean, if -- if -- we're going to do that anyway to them.

BOLTON: Yes. I mean, you've already got the president of the United States tainting the jury pool by saying that Khalid Shaikh Mohammed is guilty and should get the death penalty. I can't wait to see the arguments before the judge on that issue.

VAN SUSTEREN: Well, it'll be -- it'll be interesting to see what happens. And there a lot of people who are unhappy about this. And of course, we're going to watch it unfold. Ambassador Bolton, thank you, as always. Thank you, sir.

BOLTON: Thank you.

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