Updated

This is a rush transcript from "The Kelly File," January 30, 2015. This copy may not be in its final form and may be updated.

MEGYN KELLY, HOST: Earlier tonight I spoke with Pentagon Press Secretary Rear Admiral John Kirby about the controversy behind this deal.

Great to see you, Admiral Kirby. Thank you so much for being here.  Can you assure the American people that these five guys do not pose any threat to the United States?

REAR ADMIRAL JOHN KIRBY, PENTAGON PRESS SECRETARY: What I can assure the American people is that we are working closely with the government of Qatar to mitigate any potential threat to the maximum degree possible. And we are aware of some re-engagement activity as you've pointed out. They have not returned to the battlefield. Of course they're still in Qatar.  We're working closely with that government to mitigate this threat as much as possible.

Another thing I say is we worked hard with the government of Qatar to develop these security assurances and we are comfortable that they are the appropriate measures that these assurances will work.

KELLY: Then how did they make contact with terrorists or with the Taliban? What we're being told is they make contact with the Haqqani Network. But if our protocols are so great, how did they make contact?

KIRBY: I'm not at liberty to describe exactly what the re-engagement activity was. So I'm not going to confirm that piece of it.

KELLY: But there was re-engagement. That's my point. So obviously there's a flaw in the system.

KIRBY: Actually, no, Megyn, it was the system in place. It was the assurances and the security measures that we put in place that allowed us to discover the re-engagement activity. And so the assurances actually are working the way they're supposed to work.

KELLY: So we don't shut down the opportunity for these five guys to make contact with other terrorists. We just have a system in place to know about it. But that's a little disconcerting. I mean, that's what I hear you saying. That's a little disconcerting. I mean, should they be allowed to have this communication in the first place?

KIRBY: Well, obviously we don't want them to have communication with former Taliban whether they did or didn't let's not get into that. But we don't want that. Of course the system worked. We were allowed to discover the re-engagement activity and working with Qatar to shut it down.

KELLY: Just to round back to my first question though, I hear you're unwilling to say explicitly these guys are not a threat to the United States. We're doing our best to mitigate the threat. We're solid. We're working with the Qataris, but can you say definitively that they're not a threat?

KIRBY: Nobody said these individuals didn't have a dangerous past and could potentially have interest in a dangerous future.

KELLY: Here's the problem. One of the problems. Qatar's only going to watch them for a year and that year is up in May and clearly they're interested in returning to terror. So what are we going to do after May?

KIRBY: Well, I can't talk again about the specifics of the security arrangements with Qatar. What I will tell you is that, and it's not just Qatar and other countries where detainees have been transferred. We work very, very closely with our partners to mitigate these threats to the maximum extent possible.

KELLY: Can they go back to Afghanistan?

KIRBY: Well, again, I'm not -- they are not free to travel.

KELLY: Even after the year?

KIRBY: Right now.

KELLY: Are they free to travel out of Qatar after a year?

KIRBY: I just can't go into the details of what the security --

KELLY: Why don't we get to know? I mean, with all due respect, why don't we get to know? These are five Taliban generals that our soldiers captured. People are worried that they are going to unleash more attacks on us. One guy is directly connected to Usama bin Laden. Why don't we get to know what the procedures are?

KIRBY: I do understand the curiosity, I do understand the concern.  Believe me, we are all mindful of the threat, we exist to help defend the American people. Sometimes the best way to do that is to not talk about the specifics of security operations.

KELLY: I know you're aware that over at the White House they were questioned about the Taliban and whether this is a terrorist group. They refuse to label it as such. Do you think the Taliban is a terrorist group?

KIRBY: From a military perspective we consider the Taliban and Afghanistan as an armed insurgency. Now, as I understand it the State Department has not designated them as a foreign terrorist organization.  Yes, they use terror tactics and have use them and will probably continue to use them. They're not designated as such.

KELLY: Right, but the Commander-in-Chief George W. Bush back in 2002 did designate them as a terrorist group. So do you follow what the State Department says, or do you follow what the commander in chief says?

KIRBY: The State Department is the agency in charge of designating these organizations as such.

KELLY: As foreign terrorist organizations, right? FTOs. But the president in July of 2002 President Bush issued an executive order that specially designated global terrorists and included the Taliban as a terrorist group. I don't understand why the Pentagon wouldn't come out and say, yes, they're terrorists.

KIRBY: Megyn, let's not stand on too much of the rhetoric here.  They're an armed insurgency, they remain a dangerous group. We're aware of that. And that's why we have troops in Afghanistan now.

KELLY: Yes. I mean, that is a good point because the bottom-line is, should we have been negotiating with them on prisoner swaps? Because we don't do that with terrorists groups. Should we be doing that with the Taliban?

KIRBY: Well, in this case Sergeant Bergdahl was being held in prisoner of war like status and we were negotiating with an armed insurgent group that was recognized in that regard to get Sergeant Bergdahl back.  And I'll tell you another thing, we absolutely standby that decision to get Sergeant Bergdahl back.

KELLY: If they'd been a terrorist group, if they'd been a terrorist group, would it have been OK to do that?

KIRBY: We do not negotiate with terrorist organizations.

KELLY: See, so that's why the distinction actually does matter. And so you're asking the American people to say, this was okay because the State Department hadn't labeled them a foreign terrorist organization even though the president of the United States and the commander in chief did label them a terrorist organization. And that designation stands.

KIRBY: And from a military perspective we consider them an armed insurgency. We can go around and around about the history here.

KELLY: I know. But don't you see the aggravation for people who say, wait I thought we didn't negotiate with terrorist groups. And now they're trying to say, it's an armed insurgency and look at that, you know, designation isn't there and the American people say come on, you did it, you negotiated with terrorists. Just admit it. Tell us why it was worth it.

KIRBY: We've been talking about them being an armed insurgency from the very beginning even before Sergeant Bergdahl was involved. We believe it's really important and it sends a strong message to our troops and our families that we're not going to leave a soldier behind.

KELLY: Another question for you. We saw testimony this week from General Jack Keane, General Mattis and others, three four-star generals before the Senate Armed Services Committee that followed up on earlier statements we had heard from the now recently retired head of the DIA, the Defense Intelligence Agency. All of which said, we don't have a strategy for winning what they all consider to be a war against radical Islam -- that that's the enemy, that it needs to be identified as such, and that we need to come up with a strategy. Do you agree with that assessment?

KIRBY: What I would say is we do have a strategy to go after groups like al Qaeda. We do have a strategy to go after ISIL. We're executing that strategy and it is showing success --

KELLY: That's -- I'll give you the floor. But this is what they were saying. They were saying this is what we shouldn't be doing. Cherry picking groups, trying to do whack-a-mole, that's Al Qaeda, that's ISIL, that's this one. They were saying, let's admit the truth as they say it is we're at war with radical Islam. And we need a global strategy for dealing with that. Do you agree with that?

KIRBY: From the Pentagon's perspective we do have a strategy to go after al Qaeda and we are prosecuting them. And we have a strategy to go after ISIL and we are then. And we've been open and honest about who these people are, the ideology they espouse. Nobody here in the Pentagon is running away from the fact that these guys have an extremist view of the Muslim faith and that they are perpetrating barbaric atrocities on people in the name of that faith. We're also mindful that however good we are and however powerful we are from a military perspective, it's never going to be enough to completely eradicate this wicked ideology.

KELLY: Well, it's not even about eradication. I mean, General Jack Keane laid out the facts that Al Qaeda, that that group and its followers and its factions has grown fourfold over the past few years and ISIS has grown tenfold.

So, it's not about eradication right now. It's about stopping the cancerous growth, the metastasis. And these generals testified we're not doing it. We're failing.

KIRBY: Well, look, we know that they have fairly evangelistic view.  Particularly ISIL, they do want to spread this radical ideology. And that's why we've been saying again here at the Pentagon that what really has to happen is good governance and stability and security and options for people so that they're not attracted to this ideology. And you can't get there at the barrel of a gun. No bomb is going to completely eradicate this kind of ideology. You've got to have political solutions.

KELLY: They said that, too. They agreed with you on that last point.

Before I let you go, do you agree though with the one point that we're at war with radical Islam?

KIRBY: We are at war with groups like Al Qaeda --

KELLY: You won't say it.

KIRBY: We're at war with a group like ISIL.

You have to understand, Megyn, I'm talking from a military perspective.

KELLY: I know, so were they. So, were they.

KIRBY: When you say we're at war, we mean in a kinetic fight and we're in a kinetic fight.

KELLY: So, were they. General Mattis was a former head of CENTCOM, I mean, these guys, they are military guys, there are four-star generals.

KIRBY: I understand.

KELLY: They say we're at war with radical Islam. And so far the administration won't say that and you know, you're here representing them in part and you won't say it either, correct? I mean, you won't go that far?

KIRBY: I'm representing the Pentagon and the Defense Department. And we are at war with ISIL in the same way that we are at war with Al Qaeda.

KELLY: Okay. Listen, I appreciate you coming on the program. Rear Admiral Kirby, thank you. And thank you for your service.

KIRBY: Thank you.

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