Risen is now a senior national security correspondent at The Intercept where his incredible inside story has now been published. We talked with Risen about his career at the New York Times in a special edition of Intercepted. Below is the transcript of that conversation.

But it isn’t just the government that Risen had to fight. He also battled his own editors and other powerful figures at the New York Times. Some of those people pushed the narrative that Iraq had WMDs and they regularly colluded with senior officials at the CIA, NSA, and White House in an effort to kill — or delay publication of — Risen’s stories. James Risen has now written an extensive account of his years at the New York Times and he names names.

James Risen is a legend in the world of investigative and national security journalism. As a reporter for the New York Times, Risen broke some of the most important stories of the post 9/11 era, from the warrantless surveillance against Americans conducted under the Bush-Cheney administration, to black prison sites run by the CIA, to failed covert actions in Iran. Risen has won the Pulitzer and other major journalism awards. But perhaps what he is now most famous for is fighting a battle under both the Bush and Obama administrations as they demanded — under threat of imprisonment —the name of one of Risen’s alleged confidential sources. In the end, Risen prevailed and refused to testify and he was not locked up. But during the course of his case, there were rulings that could have far reaching implications for journalists, particularly in a climate where the president of the United States is characterizing news outlets as enemies of the people, contemplating arresting reporters, and is conducting at least 27 leak investigations. All before the end of his first year in office.

Jeremy Scahill: Jim, welcome to this special edition of Intercepted.

James Risen: Thanks for having me.

JS: So, as I read this piece, first of all, I just have to say it’s phenomenal and unusual. I can’t recall a national security reporter writing this kind of personal, autobiographical, chronicling of their time as a reporter, the challenges they face working for the most reputable newspaper in the world and fighting battles against both Republican and Democratic administrations. So, you know, I encourage people to read every word of this article.

And I’m particularly struck by what I believe is just a fact that this piece is going to be so educational and inspirational for young reporters who aspire to do the kind of work that you’ve done, Jim, as a national security reporter.

So, I’d like to start from the beginning and have you explain how you decided to become a national security reporter and how you got into all of this.

JR: My first job was in 1978 in Fort Wayne, Indiana, just as a local reporter. And then I went to the Miami Herald, and the Detroit Free Press, and then the LA Times. And throughout most of that time, I was covering either business or economics. And, I covered the auto industry, and then I came to Washington for the LA Times, and I was covering economic policy: the Treasury Department and the Federal Reserve. It was interesting for a while, but I started getting bored and I wanted to do something different.

So, in about 1995, I told my editors at the LA Times that I wanted to do something different besides economics. And they kept ignoring me for a long time and finally, said, “OK, well, we have this job where you cover the State Department Latin American policy halftime and then you can cover the CIA halftime,” because they didn’t really have a full-time intelligence reporter back then.

And I said, “OK, I’ll take that.” And then I never covered the State Department Latin American policy. I just started covering the CIA full time.

After a while, they let me just keep doing that, and they forgot that I was supposed to also be covering the State Department halftime. And, I kind of fell into the perfect time to start covering intelligence because the Cold War had just ended and the year before I started covering the CIA, Aldrich Ames had been arrested as a Soviet spy and that just caused enormous turmoil and turnover at the CIA.

And all the top people who had been reprimanded for failing to recognize that Ames was a spy for all those years were getting out of the CIA and they were all really bitter. There was a whole generation of people who really left the CIA all at once in the mid-90s and many of them were mad at the way that they had been portrayed in the press previously, because of the Ames case or whatever. And so, they were looking for somebody new to talk to, and many of them had never talked to a reporter before, but they didn’t like the press coverage that the CIA had been getting while the Ames case was going on. So, they were looking for somebody new who had never written anything about that before.

And, so, it was a perfect time for me in that I was the new guy, and they all wanted to talk to somebody — a lot of them came to me.

And the CIA was really like a high school. It was filled with cliques and little groups of networks of people and that once you got in with one or two of those guys, they would introduce you to a whole legion of people. And, so, it didn’t take long before I just found just a lot of people wanting to talk. And, it was before all the crackdown on leaks and before the government cared one way or the other about leaks of information. It was a fantastic time to cover the CIA. Also, there weren’t very many other reporters doing it back then. It was just a handful of reporters and so there weren’t very many people to compete against.

JS: How did your views shift from when you were outside looking in to when you started to, as they say in the business, make sources and get inside scoops of what was happening at the agency.

JR: Well, before I started covering it, I had the general kind of citizen’s view of it as this very secretive, imposing, intimidating place that must do all the things people thought it did, kind of the James Bond view of it. And once I got into it, I realized: these are just normal bureaucrats who are doing things that are secret. And, I realized, after a while, a lot of them were keeping things secret just because they were hiding how incompetent they were. That secrecy was really just a way to get away with things that they shouldn’t be getting away with. It didn’t dawn on me at first. That took a while for me to figure out. But what I came away with was this sense that there was — secrecy, in some cases, was valid on what they were doing, but in a lot of cases, it was more to hide politically embarrassing things or just pure incompetence or corruption.

JS: What were some of the stories that you did while you were at the LA Times or, rather, pre-9/11 that stand out to you?

JR: There was a big case of sexual discrimination by women employees at the CIA right when I was starting to cover the agency. And so, I went to the courthouse — 90 percent of the job of covering the CIA is trying to figure out how do you meet people, because they’re not supposed to meet reporters and they can get in trouble, even back then, they could get in trouble for meeting reporters. And so, the logistics of gaining access to people is a huge part of the job, much bigger part than it is for any other beat.

So, I heard that there was this class-action lawsuit by a whole bunch of women case officers at the CIA. And so, I went to the court and I started trying to meet them. I got to know some of them, and that was the first big way I got information about what was going on at the CIA.

After that, I just started going to every kind of event where I could think of where there might be somebody from the agency and just trying to find ways to introduce myself to them. And what I found after a while was a lot of these people who were now leaving the agency or were still there, they had no idea what they knew that was newsworthy. They were really kind of clueless about the larger world, which I always found very odd. I mean, they were very good at being secret agents, if you will, but they were kind of naive about the larger world, which I found astounding.

I remember this guy started — he wanted to talk about this very minor bureaucratic problem at the CIA and he went on and on about it, and in the middle of this long conversation we were having, he says, “Yeah, and is just like how Clinton gave a green light to Iran to smuggle weapons into the Balkans.” And he said, “There’s this big investigation inside the intelligence community over it.” And then he starts going back to this minor bureaucratic battle in our conversation. And I was like, I said, “Wait a second. Go back to what you just said.”

That was the first big scoop I had at The LA Times, was that Clinton had basically worked with the Iranians, allowed them to smuggle weapons into the Balkans to help the Bosnian Muslims.

I mean, you could make the case that that maybe was justifiable as an end result, but it was a — it went against all U.S. policy and international policy and so it led to a big investigation.

And then, I remember, after this guy told me about it, I went to — there was this very secretive little organization called the Intelligence Oversight Board which was, at that time, a subcommittee of the President’s Foreign Intelligence Advisory Board. Both of those are White House creations that usually never deal with the press and don’t have much to do with anything.

What I had been told was that the Intelligence Oversight Board was doing an investigation for Clinton of this whole arms channel with Iran that he had secretly set up. And I found out that the Intelligence Oversight Board was one lawyer who was a Clinton lawyer, who was a Clinton friend, who had a law office in Washington, and so the IOB was his office. And I went to talk to him, and I told him what I knew and he kept saying, “I have no idea what you’re talking about. I’ve never heard of any such thing.”

Then about a week later, the same guy called me back and said, “Now, I can talk to you about all this.” It was like this weird dance that I was doing that you as a reporter, you begin to realize, you kinda know when somebody tells you they don’t know anything about something, they really do know all about it

JS: For people that maybe don’t remember the Bosnian war, the Yugoslav civil war, just to remind people, you had Croatia, which was a Catholic republic of Yugoslavia at the time, you had Serbia, which was Christian Orthodox, and both of them had police forces that essentially converted into paramilitarized or military forces. And the Bosnian Muslims had far less weaponry and a far less robust security force, and the United States was in this position in the 1990s, coming out of the Afghan war, where the U.S.-backed the mujahideen, where the next front of jihad in the world, and jihad was not a bad word at that time, even in U.S. policy circles. In fact, among some Republicans, it was a very positive word, like Dana Rohrabacher. But the point was that the United States was in this unusual position where they were organizing donor conferences in Turkey and elsewhere to try to raise funds to arm the Bosnian Muslims. And so, at the time, the U.S. position was: This is a good thing that Muslims are coming from around the world to fight in Bosnia against the aggressor Serbs and to a lesser extent, the Croats. So, if you look at it now it’s like “Oh my god Clinton had a secret deal with the Iranians to smuggle weapons in there. but for people to remember, at the time U.S. policy was “this is a good thing to support the Bosnian Muslims in their fight against the Serbs and to a lesser extent the Croats.”

JR: That was one of the odd things about doing that story was that the end result was more or less in line with U.S. policy, but the way in which they were doing it with Iran and secretly was — it violated U.S. policy. There was an arms embargo that had been imposed by the United States and by the United Nations.

And so, it was one of those weird stories, as you’re pointing out, that you have to do the story as a story, as a journalistic exercise, rather than as something that leads to a specific outcome. And, so, you have to remember, as a journalist, you know, you just follow whatever is a good story and not worry ultimately — You can’t really try and determine what the ultimate impact of the story is, you just have to kind of find: What is a good story? What’s important to try to disclose to the American people so they can decide?

JS: I mean, it’s interesting that this big story that you did fairly early on in your life as national security reporter involved Iran and secret weapons flow, given that the Reagan administration had existed at this time of Iran-Contra where the White House had made secret deals with Iran, was using the proceeds from weapon sales to go to the contras in Nicaragua.

JR: The way I started looking into it was, “OK, is this Bill Clinton’s Iran-Contra?” And it kind of was, in a way, because if you look back at Iran-Contra itself, the end result of Iran-Contra, the objective was to free American hostages, which is not a bad thing. What is it? The road to perdition is paved with good intentions.

JS: Right. And Clinton at the time was getting hammered by the public and the world for not doing enough in Bosnia.

JR: Yeah. Yeah. Yes. One of the long-term consequences of this policy, of the secret channel with Iran, was that it increased Iranian influence in Bosnia for a while. And you look back at the war in Bosnia, and one of the long-term consequences was the rise of Islamic radicals in the Balkans. Many of the people who went to fight in the Balkans ended up in Chechnya and then, from Chechnya went to Afghanistan.

JS: Well, yeah, and many of them had, prior to that, already been in Afghanistan and it wasn’t just the Iranians, the Saudis and Wahhabi Islam. There are pockets of Bosnia now where you have this intermarrying of very radical Wahhabist Islamic fighters who then marry Bosnian women, and there are enclaves within Bosnia, they call them white Al Qaeda, these areas

JR: Yes, it’s fascinating.

JS: One of the things I also admire about this story is you don’t pull punches in your own self reflection on some of the stories that you feel that either you got wrong or that you went too far in a direction that resulted in it being unfair. I want you to tell the story of Wen Ho Lee, and for people who don’t know who Wen Ho Lee is, what was the story and what was the criticism of your reporting and how do you view it now?

JR: In 1999, I think it was, we had heard that there was an espionage case underway at Los Alamos National Laboratory. And so, we investigated and found out that there was a Chinese-American scientist at Los Alamos named Wen Ho Lee who was considered the main suspect in an espionage investigation at the time. And so, we reported that in a series of stories in 1999.

He was later arrested, and ultimately pled guilty to mishandling of classified information, but the larger espionage case against him collapsed. And the government’s espionage case basically turned out to be incredibly weak and the judge in his case said that the government should be apologizing to him for the way the case was handled.

A lot of media critics and outside critics thought that we had been way too zealous in our coverage of the case and taken up too pro-government view and too prosecutorial view of the case. And The Times, I think it was in 2000, wrote an editor’s note basically saying that we had, in some cases, been too trusting of government sources I guess or —

JS: Well, Jim let’s just read from — and you quote this yourself in the piece — you said, “the editor’s note said that we should, ‘have pushed harder to undercover weaknesses in the FBI case against Dr. Lee,’ and that, ‘in place of a tone of journalistic detachment from our sources, we occasionally used language that adopted the sense of alarm that was contained in official reports and was being voiced to us by investigators, members of Congress, and administration officials with knowledge of the case.'” You write, that “in hindsight, I believe that criticism was valid.”

JR: Yes I do. And I think it was — it was a very difficult period from me because I felt really awful about that and about the criticism. Because as anyone who has been criticized widely in public, it’s very difficult to take. But it was, you know, that old line, “What doesn’t kill you makes you stronger,” is really true and that experience, it didn’t feel that way at the time, but I’m convinced it made me a better reporter.

JS: I was a young reporter at the time working with Amy Goodman of Democracy Now!, and I was all about smashing the New York Times and Jim Risen for his propaganda, which is funny now that we work together. We’re going to get into how 9/11 changed your work and your internal fights at the New York Times, your external fights with the U.S. government. But I first want to talk to you about a meeting and an individual that you’ve cited as having an impact on the work that you would do in the future, and that’s the case of John Millis, who was a former CIA officer who then was a staff director on the House Intelligence Committee. Talk about what happened in 2000 when John Millis summoned you to his office.

JR: John was a good source of mine, and he called me and said, “Come up to my office.” So, I went up in the House Intelligence Committee space and he shut the door, and he said, “I’m going to read you a report.” He said, “Get out your notebook.”

I said, “Why don’t you just give it to me?” He says, “No, I’m not going to give it to you. I’m going to read it to you, and you take notes.”

And so, he started reading me this report, and I said, “Slow down, slow down.” And so, he let me write it out verbatim. And it was a classified intelligence CIA report from the inspector general of the CIA about John Deutch, who had been the CIA director, and his mishandling of classified information on computers and how the CIA current leadership under George Tenet hadn’t done enough in their investigation of it, in the IG’s opinion, and had kind of let him off easy.

And so, I wrote this story based on what Millis, this report. It was a big story at the time and the CIA got all pissed off because it made Tenet look bad, who was then, George Tenet was then the CIA director, because it named him and the people around him for going easy on Deutch.

And then a few months later, Millis committed suicide. And, I forget exactly how long of a time period between the two events were, but it was just a few months. And, it was weird because I went to the funeral for Millis. I was out at a church in Virginia, and I remember George Tenet was there, and I just thought this is so weird. It was like hundreds of people from the DO were there.

JS: Directorate of Operations, which is a covert action arm, that the operations in question are often covert actions that the United States never officially acknowledges.

JR: In hindsight, I always thought that must have been one of the last public gatherings of so many DO people before 9/11.

JS: Did you think that his talking to you about these secret affairs played any role in his suicide?

JR: I didn’t think so, but I wasn’t sure, and it really bothered me whether or not it had played a role. And I, sitting at his funeral, I felt really — just kind of sitting there, I felt — I was wondering what was going on. Because I was sitting there with hundreds of people from the CIA. And, ultimately, I kind of decided it wasn’t related. And for this piece, I talked to his widow, and she told me that she doesn’t think it had anything to do with — his death had anything to do with my story.

JS: And that’s another part of this sweeping story that you’ve written about your life as a national security reporter, that you interview various colleagues from the New York Times. You sought out Millis’s widow to talk to her. Because it’s the first time that you’re revealing that he was your source. And you talked to his wife about, essentially whether that was OK and what she thought about his death and whether it had any connection to your work.

JR: Yeah, I wanted to ask her if it was OK to mention that he had been a source. He’s been dead for 17 years. She said it was OK, and she thought his death had nothing to do with this.

It was nice to talk to her about it. It provided some closure for me.

JS: I just want to read another section of this for people and then, Jim, ask you to expand on it. You’re talking about when you first sort of entered the realm of reporting on the CIA and the secrets kept by government officials working for various entities. You write, “I discovered that there was, in effect, a marketplace of secrets in Washington, in which White House officials and other current and former bureaucrats, contractors, members of Congress, their staffers, and journalists, all traded information. This informal black market helped keep the national security apparatus running smoothly.” And then, later, you say: “It felt a bit like being in the matrix.”

JR: Yeah. I’m sure you know exactly what I’m talking about. It’s weird because it takes a while to get into that world, and you’re not immediately accepted into it just because you’re covering that beat. You really have to prove that you are breaking stories and that you’re, kind of, getting information out that is important.

And then you begin to find that people are contacting you and are willing to talk to you because they know that the information that they’re providing you will get out. And, it’s just this weird — it’s like joining something without realizing that you’ve joined it. It’s a very strange subculture that. And, once you’re in it, it’s very hard to explain it to other reporters who are doing other beats, like —

JS: It’s like the covert Hotel California.

JR: Yeah, yeah! And I began to feel like I had more in common with those people than I did with other reporters off the New York Times or the LA Times who weren’t involved in it.

JS: I came at this sort of a different way from you, Jim. I probably was someone that none of those types of people would have wanted to talk to, but when I started writing about Blackwater, the fact that so many people within the U.S. military and the intelligence community despised Erik Prince and Blackwater, it was sort of an enemy of my enemy was my friend, and people are people. And so, I’m in this bizarre world that you’re describing also, where I also am in contact with people that I think would never talk to me in a different setting, but because there was this common thing that both of us were interested in investigating, it brought us together in a marriage of convenience.

JR: It’s always a marriage of convenience. I mean, there’s a few people from that world that become friends, but very few. It’s a very dangerous world, because trading secrets, you’ve really got to know what the balance, what the edges of what each specific relationship you have with each person.

I always found myself, when I would go to a meeting with somebody, I would be thinking: How far can I push this conversation with this specific person based on my past experiences with this person? And it was a very transactional thing that is exhausting in a way.

JS: You’re also describing a period where there was not this intense crackdown on whistleblowers and prosecutions that happened under Obama. And some of them, of course, including your case started because of reporting you did under Bush.

One of my favorite vignettes in your story is about a woman who clearly worked in a sensitive position somewhere within the national security apparatus that called you a number of times, and to this day, you still have no idea who that woman is. Explain what happened there.

JR: It was so weird because back then, I mostly used my landline at the New York Times. And I had a cell phone, but it wasn’t something that I used in the same way I do today. And so, this woman called my landline; she obviously knew my landline number from somewhere. And she just started talking about, “I want to talk to you because I’ve read what you’ve written.”

And she went into great, incredible detail about certain things that I still don’t feel comfortable describing what it was about because I don’t want anything to lead back to her. And then she just hung up.

And then a week later, she called again. I was so worried about missing her call, that I was hanging around my desk all the time. And finally, I just said, “Let’s set a time, the same time every week, where you can call me.” And so she agreed to that. And even though I kept trying to get her to give me her name or where she worked or anything, she wouldn’t tell me anything. She was really smart.

I kind of guessed — I could guess what agency she might be with, but I wasn’t sure. And she just kept calling. And so, once a week, at a very specific time, she would call me. And that went on for several months, and we would have this weird phone relationship where we knew we had this very kind of intimate communication because it was all about top-secret information, but I had no idea who she was. And then, she would abruptly end the call every time. Then, she would call every week at this exact same time. Then finally, she just stopped calling.

I had no way to reach her. She was very careful about where she called from. And so, to this day, I have no idea who it was.

JS: That’s really a phenomenal story. I have to admit, it’s not the first time I’ve heard of this tactic used by sources, and so, full disclosure, Jim, I have heard this from other people as well. It’s never been asked of me, but you also had to strip butt naked in order to get information from another source at one point.

JR: In I guess, it was early 2003, right before the invasion of Iraq. At the time, I don’t know if it’s still true, the U.S. Central Command, it’s forward headquarters was in Qatar. So, Qatar was like, the base for our invasion of Iraq.

And so, I got this call from a long-time source who told me there’s somebody you should talk to about Qatar and Al Qaeda. And that source introduced me to another source in Europe. And then, that source introduced me to this third person and said, “They’ll meet you in Dubai.” It was a luxury hotel in Dubai.

And I contacted the person I was supposed to meet, and he told me to go to the steam room and come in totally naked because he was afraid that I would be recording him or that somebody would see us, or that somebody might overhear it.

And he told me the whole story of how Khalid Sheikh Mohammed had been protected and given sanctuary in the 90s by Qatar. And that when the CIA and the FBI found out that he was there, top officials in the Qatar government tipped him off and he fled to Afghanistan, where he started working on the 9/11 plot with Al Qaeda.

But, it was such a weird experience because I couldn’t take a note book into this meeting. And I couldn’t — he was so frightened by any microphone or anything. So, it was a weird experience.

JS: It’s like an extreme version of that scene in “All the Presidents Men” about Woodward and Bernstein and Watergate where Bernstein and Woodward are meeting with this woman who is a source and uh, they don’t want to appear to be taking notes. So Bernstein keeps going into the bathroom to write the notes down and reappearing.

But I think yours is a bit more extreme there, Jim. We’re going to talk about that story, how the New York Times dealt with it internally, and also the U.S. government, but let’s kind of start with a bigger picture. 9/11 happens and it definitely changes the course of your reporting and it ends up very quickly putting you in the crosshairs of the justice department under Bush and then eventually under Obama. Talk about the reporting you were doing in the early stages, post-9/11, and kind of the beat you found yourself on.

JR: You know, as I said, I’d been covering intelligence for about five, six years before 9/11. And so, I knew everybody. I had a lot of sources at that moment when 9/11 happened. And so, it made it much easier for me to start into the whole Al Qaeda coverage, 9/11 coverage.

But what began to happen was that the Bush administration began to use 9/11 as a justification for trying to get the press to hold or kill stories. And they began to call the New York Times, all the time, saying, “Don’t write this story. Write this story. Don’t write this story.” And that began to hit me pretty fast.

One of the first ones after 9/11 that I was working on was we found out, I think it was in 2002, that the CIA had set up a secret prison in Thailand. And it was the first secret prison. And the White House called the Times to kill that story.

That was my first experience with this whole process that later became such a major full-court press by the Bush administration.

JS: And just for people to remember, Jim, at the time you learned of this secret site in Thailand, many people will know these as black sites, the program was in its early stages where the CIA and Dick Cheney, the vice president, had a lot of hands-on experience in building this program. They were starting to develop these black sites in a number of countries where they could secretly take prisoners for interrogation, and, in some cases, outright torture. But you had learned of this before it had come out into the public light. What happened when you started trying to report that story in 2002?

JR: Well, I called the CIA for comment, and, somebody, I’m not sure, from the White House, called the editors in New York. And I’m a little confused about exactly who, but it was interesting because I know that the story was killed.

In the 2014, Senate torture report there’s this strange footnote that talks about that, about how the White House, once they found out that — it just says “a major American newspaper found out about this secret site.” It says that Cheney wanted the New York Times to kill it. I don’t know if he personally called, or someone else called, because I think they talked to Gerald Boyd, who’s now dead. But, what it says in the Senate torture report was that was the reason they moved that prison out of Thailand, which I never realized that until I saw the Senate torture report.

JS: So, was the story never ever published, Jim?

JR: I kept pushing for ways to get some of it into the paper. I got a little bit of it into the paper about a year later, but I don’t think anybody noticed. And so, by the time the Washington Post broke the secret prison story, I kind of felt like I had had that story but, I guess you could make the case that I didn’t, so.

JS: See, what I find amazing about this story and others we’re going to get to in a moment, about what happened to a bunch of your stories at the New York Times, where you have very senior people at the New York Times meeting or speaking to administration officials or intelligence officials, in secret, sometimes with the understanding that they weren’t going to share with you anything about the discussions that they had with government officials, even though you were the reporter on the story.

And, at the same time, the New York Times was taking information from these, in some cases, very same senior officials, and publishing it as part of the administration’s drive to war in Iraq.

JR: It’s because of that, that’s why I finally rebelled against the system there and why I published my book, State of War. And why I just — that’s why I finally said, “Enough, I’m not going to keep doing this.”

JS: You had numerous stories that were either killed or altered as a result of senior people at the New York Times essentially negotiating with the very people you are supposed to be very vigilantly reporting on and holding accountable. And, eventually, then you get to a point where you say, “I’m not going to play this game anymore.” And so, you can talk about the NSA story and I just want to make sure people understand, you’ve been battling for a sustained period of time against your own editors and the Bush-Cheney administration.

JR: Yeah. So, by 2004, I had gone through this process several times, and I also had stories, before the war in Iraq, about the pre-war intelligence where I talked to people who said that they were skeptical of the intelligence. And those stories had been held or killed or cut.

So, finally, in 2004, I had this person I was talking to. At some point, the source says to me, “I know what I think is the biggest secret in the government. But I can’t tell you what it is. I am too nervous.” This is like in the spring of 2004. And I said — well, I just made a mental note that I better come back to this guy and try to figure out how to get him to tell me whatever he wants to talk about.

And so, I arranged to talk to him on a fairly regular basis and finally, in the late summer of 2004, I saw this person, and I said, “You’ve got to tell me now, what the hell are you talking about?” And so, this whole story just spilled out about the NSA Domestic Spying Program, what we now know as Stellar Wind, which is the basis for the whole post-9/11 surveillance of Americans and, in about 10, 15 minutes, he just explained, basically, the whole thing.

JS: To remind people, this is a decade before Edward Snowden’s revelations.

JR: Yeah. Yeah. It’s basically the outlines of what Snowden later revealed.

JS: But what I want people to understand here, Jim, that I think is so important about your story is that, in the case of flawed pre-war intelligence in Iraq, warrantless spying, the vacuuming up of Americans’ communications, the vacuuming up of Americans’ banking data — you were aware of these activities a decade before Edward Snowden. And a coalition of very powerful government officials and very powerful senior people at the New York Times suppressed your reporting on these vital issues that could have phenomenally changed the public discourse a decade before Edward Snowden’s name was known by anyone except his immediate family.

JR: Yeah, well that’s pretty much true. We finally got a lot of it out but it took a while. A lot of it was because of, I finally decided to put it in a book because The Times wasn’t publishing the story. That was what happened with the NSA story. I, I was able to confirm with other sources what this guy was telling me about the NSA. And then I was able to, I found another reporter in the Washington Bureau, Eric Lichtblau, who was hearing similar things and we began, we wrote a story that was ready to go right before the election of 2004, between Bush and John Kerry, and the New York Times killed it because The White House asked them not to run it.

We had these, a lot of arguments at the paper at that moment about it. We had a big meeting in New York over that, I describe in the piece. After the election, Eric and I, got them to agree to let us try again to report it. We re-reported it and re-wrote it, then, they killed it again. And, so I went on book leave and I decided, “I’m going to put everything I know in my book.” And so, I put that story and then another story they’d killed, on a crazy CIA operation in Iran in my book. And, after I’d finished writing the manuscript, I told the editors in the late summer of 2005, “I’m putting these stories in my book. You should publish them.”

And, then, that began a whole another, several months of very difficult negotiations between me and the New York Times and the New York Times and the Bush administration.

JS: Talk about these meetings that senior New York Times people were having with powerful government officials about your reporting. Tell some of those stories and who the characters are?

JR: At the time, Bill Keller was the executive editor of the New York Times, and he had made the decision before the election of 2004 not to run the NSA story. And Philip Taubman was the Washington Bureau chief and he had agreed with Keller’s decision.

After the election, the second time when we had tried to get it, we met just with Taubman, not Keller directly, and Taubman decided we shouldn’t run it, I’m sure with Keller’s consultation.

And so then, in the fall of 2005, when I told them, “This is all going to be in my book,” everything about the NSA story and the CIA-Iran story, and they should run them, they got furious with me. They were just outraged that I was doing this. And Taubman thought I was being insubordinate. We had some very difficult meetings between him and me.

And what I didn’t — then, they started having negotiations directly with the Bush administration, Taubman and Keller in particular. And they thought because I was being insubordinate, I couldn’t attend these meetings. And the year before, in 2004, when they were thinking about running it, they’d also had meetings with the government. And there’s one in particular that, right after the election, when we were reconsidering trying to run it in November, December of 2004, when Taubman went with Michael Hayden who then was the head of the National Security Agency, Hayden brought Taubman out to the NSA and actually had to meet with people who were actually directly involved in the domestic spying operation, and had them explain exactly what they were doing.

And he did it on what he describes as an off-the-record basis and he considered that off-the-record basis to mean he couldn’t tell me and Eric Lichtblau what they told him. And that was a real point of serious contention.

JS: Just so people can follow this, because there’s names and entities, et cetera: Your editor at the New York Times, Phil Taubman, developed this apparently closer relationship or a mutual-based trust relationship with the NSA Director Michael Hayden, and you had your own editor going and meeting with the head of the NSA and being taken on these tours meant to terrify him into not publishing your stories. I mean, it’s, to me, it just seems like a kind of unconscionable crime against journalism to do that.

JR: Well, I agree. You know, that’s what happened. And one of the things I found in doing the reporting for this piece which I hadn’t read before, I read part of Mike Hayden’s memoir that came out last year, which was not high on my reading list before this. But he says in there something fascinating to me.

There was a meeting that I went to before the election with Taubman. It was Taubman and I, and we met at the White House with John McLaughlin, who was then the acting CIA director, and John Moseman, who was his chief of staff, and they were trying to get us not to run the story. That was the very first meeting than anybody from the New York Times had with the government over this story.

And what I had never heard before, until I read a small passage in Hayden’s book was he said, “McLaughlin sent me basically a readout of this meeting, in which he said, I think we can work with — Taubman was very respectful and understood the issues and Risen, clearly, all he kept talking about was the public’s right to know, and he didn’t give a shit about what we were saying.”

And so, Hayden writes in there, “I decided we could work with Taubman.” And so that, to me, made it clear that what was happening ultimately was they were trying to, in the words of, the CIA would call that “case officering,” which means you’re trying to seduce somebody.

JS: Well, and clearly it worked, or at least, it was very effective in delaying publication, and, in some cases, excising parts of your reporting from the published pieces.

JR: Yeah. So, you know, ultimately, I decided the only way the story would ever see the light was to put it in a book. And I realized that would probably mean that I would get fired from the New York Times, and that was the decision I had to make.

I told my wife, “I’m probably going to get fired for this.” And she said, “Well, if you don’t do it, I won’t respect you. So.”

JS: I want to back up for one second on something and get your take on this. You describe in this piece, also, some of the reporting that you did about flawed or wrong intelligence in the lead-up to Iraq, that was either not run by the New York Times or was buried inside the pages of the paper. Did you get a sense at the New York Times at the time that there was a support, at high levels, for the drive to war or the narrative that there were in fact, weapons of mass destruction in Iraq? I mean, if you look at how Michael Gordon and Judith Miller’s pieces were, you know, multiline headlines, put on the front pages, versus yours being cut or buried?

JR: Yes, absolutely. There was no doubt at the time. There was the atmosphere within the paper was: We want stories about the existence of WMD and we don’t want any skeptical stories. And, at the time, the word was that was what the top management wanted. And no one would come out and explicitly say that, either then or now, but I believe that was the case.

And, I think that was one of the things that I feel bad about is how so many, how people outside the New York Times personified the criticism about it and made it about Judy Miller, rather than as a systemic problem. I believe it was a systemic problem at the paper, and it wasn’t — Judy couldn’t get her stories on page one by herself.

JS: Right, it’s a fair point and I know also in her memoir, she also believes that the fact that she was one of the most prominent female journalists, and the field that you and I are in, Jim, has long been dominated by white straight men.

JR: I say in the piece, I believe that she was the victim of gender bias on that.

JS: Right, I think that two things can be true at the same time, I agree with you. I mean, Michael Gordon was bylined on lot of those pieces that didn’t get nearly the level of blame for that Judy Miller did, which brings up another issue regarding Judy Miller. She, of course, was the only reporter, correct me if I’m wrong, the only reporter or journalist that actually went to jail for their refusal to give up a source in the Valerie Plame investigation. And, just to remind people, Valerie Plame was a CIA officer who was on non-official cover and was working on the WMD investigation. Her husband, Joe Wilson, was the former U.S. ambassador to Iraq, and had gone over to Niger to investigate these reports of yellowcake uranium and then wrote an op-ed about what he didn’t find in Niger. And then, this targeted campaign to smear him was orchestrated very high levels of power within the Bush administration, and then you had Bush officials going around town with a whisper campaign, that was much more audible than most whispers, saying, “Oh, by the way, his wife is an undercover CIA agent, or operative.”

And Judy Miller was one of the reporters that had heard this. We now know that her source was Scooter Libby — at the time, the senior aide to Dick Cheney. Sorry, for all of that background, I want to make sure people are with us here.

It’s interesting when you juxtapose this though, and this is what I wanted to ask you about, the way that this case was handled, where you had a retaliatory act committed against an undercover CIA officer, because her husband was blowing the whistle of some of the fraudulent claims being made by the administration. And I think a lot of people on the left were team special prosecutor there, that Judy Miller is on the wrong side of this and we need to know who in government is running around giving up the name of an undercover CIA officer.

And then, in your case, Jim Risen is being unfairly put into a position by the justice department where they’re trying to force him to give up his source on a story that also cast the Bush administration in a damaging light because of secrets that they were trying to keep about a variety of covert actions. How do you reconcile those two things? Because the Fitzgerald prosecution and the fact that Miller actually went to jail for this is interesting when you then look at your struggle and your battle on the very same issue: I will not give up a source.

JR: Yeah, and I think that the liberal position during the Plame case was a big mistake, because people in Washington were generally looking at the Plame case as a proxy for a debate over the war in Iraq. And what they weren’t looking at it as was a fight over press freedom. And, ultimately, I think the unintended consequence of the Plame case, was that it damaged press freedom in the United States. Because as a special prosecutor, Fitzgerald didn’t have to get approval from the attorney general to subpoena reporters, he could do it on his own. Normally, prosecutors have to go through the attorney general media guidelines to decide whether a case rises to the level of requiring a subpoena of a reporter.

And so, as a result, Fitzgerald just blew through whatever limitations there had previously been on going after reporters in leak investigations and he basically ended 30 years of informal understanding that had existed between the press and the government over how the government dealt with leak cases.

And so, I think that the unattended consequence of forcing not just Judy, but a lot of other people into the situation, was ultimately led to what happened with me and other cases since then. It convinced the government that they could go ahead and go after reporters and go after sources and that there would be no real political backlash. And I think that was a major legacy of the Plame case which no one saw at the time.

JS: I do think you are right. And again, two things can be true at the same time. You can, on the one hand, find it risible or despicable that reporters would play along with this kind of a campaign from the vice president and his minions, and probably others, and think that’s awful, and at the same time say, “wait a minute, we’re going to set up very dangerous precedent here if we believe that reporters under any circumstances should be forced to give up their sources.”

JR: That’s exactly what happened. And I think no one thought very clearly about that at the time. And Judy Miller was a very controversial figure by that point, because of the WMD coverage. And so, it was difficult for very many liberals to get behind supporting her publicly. And no one wanted to support the Bush administration and the White House, in their effort to hide what really had to happen in the leak on Plame. But, ultimately, Fitzgerald used that political support I think he had, to just bulldoze whatever informal understandings we had and they’re now gone.

JS: So, for people that didn’t follow this, explain what was happening to you under the Obama administration, the Justice Department at the time, and why you were at risk of potentially going to jail?

JR: The New York Times finally ran the NSA story in December 2005 after I told them it was going to be in my book. You know, we had these long meetings that I described. And finally, they ran it.

Then, my book, “State of War,” came out in early January of 2006. And one of the stories that had been held by the New York Times that I had put into that was another story, it was about a secret, crazy, screwed up CIA operation involved Iran and its nuclear program and the New York Times had never run that, even though they ran the NSA one. I told them it was going to be in my book but they never got around to considering running it.

I believe what happened was that the Bush administration started two leak investigations: One of the NSA story in the New York Times and a second one about my book, and things that were in “State of War.” And I know that they had FBI agents talking to people about several different chapters that were in my book that were not in the New York Times, and I believe what they were doing was looking for something they could get on me separate from the New York Times.

And, finally, they decided on the chapter about the CIA-Iran story. And they dropped the investigation of the NSA story in the New York Times. What I believe is that the NSA story was what really angered them, but that they didn’t want to take on the New York Times in a constitutional showdown over the publication of it.

And so, I think they were looking for something where they could isolate me. And I’ve had a lot of evidence to support that over the years from various people.

In the summer of 2007, we got a FedEx letter from the Justice Department saying, “We want to talk to you. We want all your information about your sources on this chapter.” And, so, I got some lawyers involved and began to negotiate with the Bush administration. And, finally, I refused to provide them any information, and in January 2008, they subpoenaed me to testify before a grand jury looking into that leak, and I refused to cooperate.

And, the judge, who in this case, Judge Brinkema in the eastern district of Virginia, the federal district court, I think she recognized that that was an election year and let the clock play out through a lot of procedural motions that took a long time. I think she figured, if Obama wins, he’s going to drop this case. And, so, Obama won and I thought, yeah, Obama is going to drop this case.

Then in July, I think was June or July of 2009, the judge issued a very brief memo that said, “I see that the grand jury, in this case, has now expired because it’s been so long. That means that the subpoena is now moot and I give the government 10 days to decide whether to drop this or not.” And I thought, “OK, that’s the end of this case.” And I think it was a written invitation from the judge to the Obama administration to drop this case very quietly and let it go.

And instead, Eric Holder and the new Justice Department said, “No, no, no, no, we want to keep this case going.” They issued a new subpoena to me. That was my first taste of how the Obama administration was going to continue the post-9/11 world just pretty much the way Bush had been doing it.

JS: This battle that the Obama Justice Department was waging against you in and of itself became a media circus where you had once been the print journalist who watches the huge pile-up of camera people chasing someone, and then you had to witness that in your own case from either side.

JR: Yeah. It was bizarre to become a subject of the press. It’s actually a very humbling experience because I think it’s actually good for every journalist to be the subject of a story once, it makes you realize how flawed we are as reporters. But, yeah, it was weird because finally, for the most part, except for a few print reporters, media reporters, the press ignored my case until 2014 when it went to the Supreme Court. And when the Supreme Court finally had to decide whether to take the case, that’s when it finally started getting a lot of attention.

And when the Supreme Court refused to take the case, that meant that I was either going to have to testify or go to jail. And I refused to testify and there were no more legal options available and so then the pressure began to build on Eric Holder and the Justice Department of whether they really were going to send me to jail or not.

Finally, in early 2015, they caved and decided not to. They had a pre-trial hearing, where they forced me to come in and say in person whether I was going to testify or not. And I told them, “No.” Then they said, “OK, that’s it.” And then they blinked at the last minute.

JS: I would also encourage people to go back and listen to the first appearance of Jim Risen on Intercepted where we talk in-depth about that case. Jim, final thoughts here from you on the battle of reporters versus the government on this issue of secrecy. I’ve been recently re-reading some of the history of Nixon’s ideas on how to go after people like Seymour Hersh. You’ve had battles going back to the Progressive Magazine, publishing documents on making a hydrogen bomb. There have been huge battles over national security and government secrets between journalists and those in power. And it’s not Democrat or Republican; it’s those in power, whoever they may be.

Your thoughts, though, about where we are and where we’ve been, this fight for a truly independent press that believes in holding those in power accountable.

JR: I think the post-9/11 world has been very difficult for that. And I think the press has been far too deferential since 9/11 to the government, and it’s made the government realize they can use the word “terrorism” or “national security threat” for almost anything. And it’s made the press much more docile, and I think that is something that has to be fought back against.

I think the New York Times has gotten a little better about it since my case. I think the NSA story and my whole experience on that helped force them to get all better about it. But, generally, the press is still way too deferential and is so cowed by the perceived and supposed threats from terrorism that they are willing to go along with the government in ways that I don’t think they should. Part of it’s also because of the financial condition of the press.

They’re so weakened, they’re so fragmented now, that there’s no great role models in the press anymore that everybody will follow. Individual reporters have to be willing to stand up themselves because institutions today are, generally, too weak to do it. And so, it really comes down to, as a reporter, stand up for your own story. If you do, you’ll ultimately be proven right.

JS: I would just add Jim that I think it’s also incumbent upon all of us as journalists to stand up when any journalist is put through the ordeal that you were. Because it’s very shortsighted to just say, “Well, I’ll be there when my friends or the people that I agree with are in the target sights of the powerful.”

Jim Risen, thank you very much for all the work that you’ve done and for this incredible piece at theintercept.com. I encourage everyone to read it, particularly, young people who are interested in doing the kind of journalism that Jim Risen has done for so long and continues to do. Jim, thank you very much for being with us.

JR: Thanks very much for having me. I appreciate it.

JS: James Risen is a senior national security correspondent at The Intercept. He was a long-time national security correspondent at the New York Times, where, among other awards, he won Pulitzer Prizes. You can read James Risen’s complete story at theintercept.com.

[Musical interlude]

JS: And that does it for this special bonus episode of Intercepted. We’ll return with Season 4 on January 17th. If you’re not yet a sustaining member of Intercepted, log onto theintercept.com/join. Intercepted is a production of First Look Media and The Intercept. We’re distributed by Panoply. Our producer is Jack D’Isidoro, and our executive producer is Leital Molad. Laura Flynn is associate producer. Elise Swain is our production assistant and graphic designer. Our music, as always, was composed by DJ Spooky.

Until next time, I’m Jeremy Scahill.