Thomas Drake, a brilliant intelligence analyst, software engineer, and IT management consultant, worked at the CIA in the 1980s, then as a contractor at the National Security Agency (NSA), and ultimately as an NSA senior executive in 2001. But from 2006 until July 2011, he became the government's and NSA's public enemy.

Why? From his high-level perch at NSA, he saw the failure to act on intelligence that might have prevented the 9/11 attacks, and he saw corruption at the highest levels.

So he blew the whistle. Four times, from the fall of 2001 through 2004.

Once to both the House and Senate Permanent Select Committees on Intelligence. Once to two Congressional investigations seeking answers to the intelligence failures surrounding 9/11, including what NSA knew, didn't know, could have known, and did or didn't do. Drake was asked to be a material witness for a Congressional investigation, initially led by then-Rep. Saxby Chambliss (R-GA). He was instructed not to tell NSA that he was cooperating with the investigation.

The fourth time was in September 2002, when Drake submitted a complaint through a Department of Defense Inspector General (DoD IG) "Defense Hotline" that allows whistleblowers to report fraud. The call launched an audit of the way NSA awarded multibillion-dollar contracts and managed some of its programs. This time, Drake first alerted supervisors, who either sat on the information or pulled him off key assignments.

When the DoD IG audit went nowhere, he took what he knew -- none of it classified -- to The Baltimore Sun.

After Drake went to the media, the FBI raided his home in 2007, seizing computers, books, and other material.

Ultimately, he was cast from the intelligence kingdom and charged with 10 felony counts in April 2010, five under the 1917 Espionage Act. "I got in the way of the power structure," he explains.

Some of his story appeared in newspapers, The New Yorker, blogs, and a 60 Minutes segment, describing how the FBI raided his home and dug for documents to prove he'd passed information to two New York Times' reporters about the White House illegal wiretapping program and other offenses. Although the FBI never found such evidence, the Justice Department indicted him.

I asked Drake if there was more the public had to know. "Definitely," he said, but under the government-initiated plea negotiations, he couldn't say anything new until after his sentencing date last July. Otherwise, the government could have used it against him at the trial.

Once the case against him collapsed, prosecutors agreed to drop all 10 counts against Drake; he pled guilty to a minor misdemeanor for "exceeding authorized use of a computer [!]," with no jail time or fines.

The result, however, was a life severely wrecked. Drake has worked at an Apple store since August 2009.

This is what he told us.

Barbara Koeppel: What did you tell the Saxby Chambliss Congressional subcommittee and the Congressional Joint Inquiry?

Thomas Drake: I can't say fully, because it's classified. But I showed that NSA knew a great deal about the 9/11 threats and Al Qaeda, electronically tracking various people and organizations for years -- since its role is to collect intelligence. The problem is, it wasn't sharing all of the data. If it had, other parts of government could have acted on it, and more than likely, NSA could have stopped, I say stopped 9/11. Later, it could have located Al Qaeda -- at the very time the U.S. was scouring Afghanistan.

It's true that there were systemic failures throughout the intelligence system, but NSA was a critical piece of it. I gave both committees prima facie evidence, with documents. One was an early 2001 NSA internal, detailed multi-year study of Al Qaeda and sympathetic groups' movements that revealed what NSA knew, could have done, and should have done. It was astonishingly well-analyzed current intelligence. Soon after 9/11, some NSA analysts called me about it. Why? Because they were pulling their hair out, knowing they had this information and they couldn't get NSA leadership to share the report with the rest of the intelligence community -- even though it's mandatory! It was actionable information. Remember the time period--we were in the early part of the war in Afghanistan. People needed to act on it, to unravel Al Qaeda networks.

But NSA leaders deliberately decided not to disseminate it. So the analysis -- about what it knew before and after 9/11 -- got buried very deeply, because it would really have made them look bad.

In fact, after the analysts called me to complain, I told my superior, Maureen Baginski, Director of Signals Intelligence (called SIGINT), who was the number-three person at NSA. But instead of acting on it, she got mad at me. She said, "Tom, I wish you'd never brought this to my attention."

BK: Why?

TD: Because she no longer had plausible deniability.

BK: And then?

TD: I said, Mo (that's what we called her), I'm bringing it to your attention because it's information we need to share. This is key to Al Qaeda's position. But she folded. She was going to protect the institution. Screw national security.

BK: Talk more about the Congressional investigations.

TD: The Saxby Chambliss subcommittee began its hearings in February and March 2002. It had subpoena power and contacted me off the record, because it was investigating NSA. I gave both the subcommittee and the subsequent, much larger Joint Inquiry voluminous amounts of information.

BK: What did they do with it?

TD: I don't know. There's a report, but it's classified. I never saw it. And the public got just a small version of the data I gave them. In fact, there's very little oversight in Congress anymore. When there is, it's essentially just talk.

BK: How did NSA react to the investigations?

TD: It did everything it could to obstruct them so it could hide what it knew. I remember hearing from Lt. General Michael Hayden, NSA's director, while the investigations were under way, saying how "convenient" it was for CIA and FBI to be taking the heat, while we remained in the shadows. I'm paraphrasing, but NSA knew a lot.

BK: How did NSA obstruct them?

TD: First, it asked the committee investigators to set up their office at NSA, where the agency could put minders, NSA people who would sit and take notes. But the committee refused.

BK: Other ways?

TD: NSA set up what we called the "war room," to figure out how to respond to the Saxby Chambliss investigation. The joke was, 'Who are we at war with? Congress or terrorists?'

Then in February, Mo asked me to lead an NSA team, to go around the agency pulling together information about what NSA knew that it could give to the subcommittee as its official classified statement, for the record.

So I wrote the statement, which went through multiple drafts. Later, I was in England on another assignment, and I got a frantic call from one of my staff, saying, "Tom, they pulled us off the effort and re-assigned it to someone else." I asked why. "Well, it's confusing, you'll have to ask Mo." When I got back, the first thing I did was ask her why we were taken off. She said, "Data integrity." This was a euphemism.

BK: A euphemism for what?

TD: That there was a problem with the data. But there wasn't a problem. They just didn't want it out there. Congress was asking us to take our clothes off, come clean, say we screwed up, and how we would fix it.

But NSA chose not to do that. Instead, it persisted in the cover-up and didn't tell about the staggering amounts of information it had in its data banks and didn't share. When it's being investigated, it closes ranks. To say they were not cooperating with the 9/11 investigations is an understatement.

NSA created a secret team that reported to Bill Black, the Agency's deputy director, whose task was to find the agency's 9/11 skeletons. Why? In case you're put on the stand, you want to know where you're vulnerable so you have an answer, or can create one to serve as a cover. The idea is, NSA only tells Congress what it wants them to hear, and Congress will just have to figure out what it really knows. The problem is, how will Congress find something unless it knows what it's looking for and where to find it? And if NSA can keep it hidden, Congress' chances of finding it are slim to none.

BK: Are there other ways it obstructed?

TD: A dramatic one. It happened in early 2002, when Mo warned me, "Be careful, they're looking for leakers." What she meant was, "Back off! Don't say anything more to Congress than you need to." But I wasn't leaking to the press, or outside of channels. I was a material witness in official investigations of NSA!

BK: Then why call it "leaking"?

TD: They were calling it that. For NSA's purpose, it's leaking. Me, I'm serving as a material witness to Congress, which called me to do that. I didn't go to them.

BK: If it wanted to, could NSA follow your trail?

TD: Easily. Bread and butter. That's what they do. In fact, during this whole time, NSA was doing everything it could to figure out and track who was cooperating with the investigators or called as material witnesses.

BK: Why was it so important for NSA to hide what it knew?

TD: Because NSA is a closed, secret culture. Its primary focus is collecting data, even within the intelligence community.

The coin of the realm is what you know. If I share something with you, then I don't have power any more. So why would I give my power away? Because we collect the data, we own it. If we own it, we control it. If we control it, we can say what it means. We tell you what we want to, or not. I used to hear that in executive sessions, post-9/11. Other agencies were clamoring for the raw or nearly raw data, to do their own analyses. And NSA was balking because "we don't know what they're going to do with it."

BK: But wouldn't NSA want to prevent a 9/11 or track Al Qaeda?

TD: That's logical thinking. You have to remember, NSA is an institution, and it preserves its integrity before anything else. Rule number one. It's pathological. It's what I call the deep, dark side of this culture, one that has rarely been discussed. Everything is secret. Over decades, people work, communicate, and engage in secret. Obviously, certain state secrets are legitimate, but this goes way beyond that. The agency thinks, if it gives away information, it's fragmenting its identity. In fact, even before 9/11, NSA reprimanded people for cooperating with other parts of the intelligence community.

BK: Do other intelligence agencies operate the same way?

TD: Yes. When I was at CIA, I worked in the Science and Technology directorate on the issue of weapons of mass destruction. I was asked by people at its National Photographic Interpretation Center to look at pictures of WMD targets. I agreed, but I couldn't tell from the photos who was talking to whom without knowing more about the target. So I called my buddies at NSA -- because they have electronic and signals intelligence -- to find out, and they told me what they knew. But the people I worked with at CIA said, "Why did you call them? You have everything you need right here." Well, I didn't. It's so arrogant, to say you can't learn from others. But this is the culture. And it's even worse at NSA.

Barbara Koeppel is a Washington-based investigative reporter. This article has been slightly edited for space; subscribe to The Washington Spectator to read the second part of this report, addressing evidence of corruption that Thomas Drake turned over to investigators.