This is a partial transcript from "The O'Reilly Factor," August 19, 2005, that has been edited for clarity.

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TONY SNOW, GUEST HOST: A military intelligence officer has sparked a fire storm of controversy over his claim that a Pentagon intelligence unit identified Mohammed Atta (search) as a threat to national security before 9/11, but was ordered not to pass the tip on to the FBI. This stunning revelation also is raising questions about why the 9/11 commission never even mentioned this intelligence failure in its report on Al Qaeda's attack on the Trade Towers.

Lieutenant Colonel Anthony Shaffer joins us now from Washington. Colonel, let's walk through a number of things. First, you were in an intelligence unit. Now we know the name was "Able Danger." And...

LT. COL. ANTHONY SHAFFER, U.S. ARMY INTELLIGENCE OFFICER: Right.

SNOW: And you and you colleagues had come up with the information that Mohammed Atta and three others in the so-called Brooklyn cell had been identified in the United States.

Now you personally at that time did not know who Atta was, but some of the others in the unit did, correct?

SHAFFER: Well, that was the issue. Yes, we knew these guys were bad guys. That is to say that the names of the individuals were linked to — via this technology, the linkage technology-- to Al Qaeda leadership. That was the issue, that no, we do not have any inkling these guys were up to no good.

In particular, we thought they may be because of the linkage. We didn't know exactly where they would have been at any given time. But the names, by all accounts that I'm aware of how we did this -- and again, I was there, I talked to the analyst, and I don't know — I'm not an analyst, I can't talk to exactly their techniques.

But I do know that they put this together and presented it to us as — to make sense of and to do planning against to do something with.

SNOW: Let's say in perspective what you were doing. You were really trying to come up with a roadmap to Al Qaeda, to figure out how it worked all around the globe. So you were using, as you said, link analysis, in other words, you were doing data mining. You were looking at a lot of different data. You were looking for patterns.

SHAFFER: Right.

SNOW: And low and behold, somebody found patterns about the Brooklyn cell.

SHAFFER: That's right. Now we're talking about tremendous amount of data. Two point five terabytes of data, all open source, is the beginning, laying the foundation of the operation. Then using advanced technology to look for patterns.

One of the examples of a pattern would be what did the terrorist bombers look like, pattern wise? Who did the first track on the World Trade Center in 2003 -- I mean in 1993? And then, taking that information, putting it into the computer, and seeing who else fits that pattern. That's the essence of it.

SNOW: All right, now let's take a look at what's happening since the "Able Danger" revelation came out. First thing was the 9/11 Commission (search) said was we never heard from these guys, then said they did hear from these guys. Then that the information was nonspecific or it wasn't credible, or that it was not historically significant.

SHAFFER: Right.

SNOW: Talk about your attempts to get the 9/11 Commission to listen to you, beginning in Afghanistan.

SHAFFER: Right. I met with the commission, Dr. Philip Zelikow, the executive director of the commission staff, commission staff, let's be clear here, in October of 2003 in which I presented to him and two other staff members, and an attorney, in my recollection of "Able Danger."

And the reason I know this is because I had a full talking point paper that I put together in advance of the meeting, where I did the - essentially the "who shot John," went throughout the process of telling them about how it stood up, what the authorities were, what problems we had, what we detected. And the bottom line was we discovered two of the three cells, and I'm using the exact phrase I remember using, two of the three cells which conducted the 9/11 attacks to include Atta.

SNOW: All right. What also had happened is you had this information. And the lawyers at the Pentagon told you you can't share it with the FBI?

SHAFFER: Right. To go back in history, back to 2000, yes, we tried in the summer, fall timeframe, one — the special operations command lawyers said you can't look at this, they're here legally, pretend they don't exist.

The units operation officers now identified as a Navy captain said flat out we need to do something. So he came to me and said you've got great contacts at the FBI. Can you broker a meeting so we can try to pass it?

I brokered the meetings through my unit, Stratus Ivy, which was a DI [Defense Intelligence] mission unit, which I ran. And to be totally blunt, SOCOM never showed up. And I found out later from this captain, the lawyers made recommendations to the chain of command. The chain of command accepted it. And therefore the information was never passed.

SNOW: SOCOM is a special operations command...

SHAFFER: Yes, sorry.

SNOW: ...which had overall jurisdiction over the program.

SHAFFER: Right. That's correct, sorry.

SNOW: All right now, there have been a number of reports - it's interesting to me, you're getting some pushback already from the Pentagon. One of the things that's happening is people saying well, you know, we can't find any documentation for this. What's going on?

SHAFFER: Well, that's an interesting question. I've heard rumor of a rift internally. I -- that's just a rumor. We don't know exactly what's going on, because in good faith, I met with Dr. Cambone, the Undersecretary of Defense for Intelligence, this past Monday, along with General Schwartz, the director of the Joint Staff also this Monday, where they asked us to -- asked me and my other members of the Able Danger former effort to cooperate.

I spent time with the Pentagon Tuesday, laying this all out for them. What the impression they would ask us to come back and help them look through the documents. This has not happened yet.

And my concern is how do you look for something in the way of documents and all the different issues which go with those documents to make sure you have all of them unless you have the original members somehow telling you all the things that were out there and where they're at?

SNOW: Now it has been reported that they have two briefcases worth of documents. You just talked about 2.5 terabytes. That's a small room full of documents.

SHAFFER: Just slightly. Yes, I'm aware of, based on my direct knowledge and being - talking to the other members, there are about 20 boxes of stuff just of the "Able Danger" focused information.

So historically, there's got to be some record of this somewhere. And again, we've not, to my knowledge, been able to locate my personal files. I kept one of everything of Able Danger regarding the stuff they briefed the Pentagon leadership because my unit and my office became the Able Danger forward location for storing these things. They didn't want to have to bring them back and forth between Tampa and Washington, D.C.

SNOW: Why did they shut down "Able Danger?"

SHAFFER: Good question. And I don't know if I could give you a really clear answer on that because it kind of mystified me at the time, too.

Any time you have a global terrorist target, such as Al Qaeda, which has hit you several times, we're talking about the Cole, the embassy bombings in Africa, I would think that a project where you're trying to target them globally, offensively, looking at offensive options, would be the best thing you could do try to go after and prevent and attack.

Again, we had no inkling about 9/11. And I don't want to give that impression. But as a soldier and the soldiers and sailors and air men who worked with me on this project, we knew there was an issue here that needed to be looked at. And that was -- I can't tell you what the thinking was at the leadership level to turn it off.

SNOW: All right. But that happened in the spring of 2001?

SHAFFER: Right. And I was specifically told to back out of it by an Army two-star general, where I think it's been reported. And I confirm, I was nearly insubordinate with this general by the fact that I said we need to do this. This is important.

And it came to the point where he had to remind me, formally that he is a two-star general, and I am not, and I am to do what he told me to do.

SNOW: Well, you're still a lieutenant colonel. Colonel Shaffer, thanks for joining us.

SHAFFER: Thank you, sir.

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