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This is FRESH AIR. I'm Terry Gross. New questions about alleged abuses in the Bush administration war on terror have been raised in recent days with a series of damaging revelations, including the revelation about a secret CIA anti-terror program.

The CIA hid the program from Congress for eight years, apparently at the direction of Vice President Dick Cheney. Several national news organizations now report that the program involved assembling secret hit teams to kill al-Qaida operatives in other countries.

The program, which was never operational, was recently canceled by the new CIA chief, Leon Panetta. Our guest, Jane Mayer, has written extensively about the intelligence community and the war on terror for the New Yorker. Her latest article was about Leon Panetta and whether he can move the CIA forward without confronting its past. She's also the author of the bestseller, "The Dark Side: The Inside Story of How the War on Terror Turned Into a War on American Ideals."

Mayer spoke this morning to FRESH AIR contributor, Dave Davies.

DAVE DAVIES: Well Jane Mayer, welcome back to FRESH AIR. Now the nation, of course, has paid a lot of attention in recent days to revelations by the CIA director, Leon Panetta, that Congress had been kept in the dark for eight years about a secret anti-terror program run by the CIA. What do we know about this program now?

Ms. JANE MAYER (Author, "The Dark Side: The Inside Story of How the War on Terror Turned Into a War on American Ideals"): Well, we still don't know all of the details, but it sounds like, from the reports that have been out there, that it was a program to form a kind of a death-squad unit that would rove the world in search of al-Qaida leaders who, under this program, could be targeted for killing.

DAVIES: So assassinations outside the United States, as far as we know, right?

Ms. MAYER: Well, assassination is actually a term that suggests illegal activity, and so targeted killing is what it would have been called because that suggests, then, that it was legally authorized.

DAVIES: And as far as the reporting reveals so far, never actually implemented, right?

Ms. MAYER: That's right, though there does seem to be some suggestion that the unit was set up and - but that it never became operational. I think it went - it was somewhere between an idea and an actual program. They began to take a close look into setting it up and I think maybe began to train people slightly, but those are the details that we're still trying to ferret out.

DAVIES: And is it clear that Vice President Dick Cheney was largely responsible for keeping this secret from Congress?

Ms. MAYER: Well, that is what the current CIA director, Panetta, told the committee, the Intelligence Oversight Committee, and so far it remains undisputed. So I guess we can assume that former Vice President Cheney truly did try to purposefully keep this information from Congress.

DAVIES: Now, congressional leaders are furious about this, but I'm sure a lot of Americans wouldn't necessarily expect that the CIA would talk about its most sensitive covert operations, even in closed doors with congressional leaders. What exactly is the obligation of the CIA to disclose these kinds of operations?

Ms. MAYER: Well, I mean, the problem is that there is a legal requirement that the CIA disclose these kinds of operations. It's not up to the executive branch whether to inform the congressional overseers of covert programs and other important intelligence activities.

Under statute, the CIA is required to disclose these kinds of details. There's some leeway in terms of how quickly they need to disclose them, and there's some interpretive leeway also about what kinds of programs must be disclosed, they have to be important programs, but they don't necessarily have to be operational programs. They have to even inform Congress when they are considering important covert operations.

DAVIES: Now, you and others have written about the tendency of Vice President Cheney and his chief of staff, David Addington, to take different, perhaps somewhat more innovative views, of the reach of executive power. Do we know if this is an area in which they also had a different view of the intelligence - the executive branch's legal obligations to inform Congress?

Ms. MAYER: Definitely. This is a key area where there's a long history here, a long…

(Soundbite of laughter)

Ms. MAYER: …and very fraught, basically, where former Vice President Cheney has resented the role of Congress in overseeing intelligence operations and in, as he sees it, interfering in the executive branch's right to conduct national security and foreign affairs.

So this goes way back - we're talking about to the 1970s, basically. So maybe it's worth sort of filling in some of the history here, if you want.

DAVIES: Well you know, and the history involves what were then called assassinations, which as you say now, targeted killing may be the preferred term, but back in the '70s, there was an enormous outcry about the CIA's activities abroad that involved killings of perceived enemies of the United States. It's led to, you know, the Church hearings in Congress and new rules for this. To what extent are we…?

Ms. MAYER: Specifically, those kind of activities, which is the irony here, it's specifically reports of assassination attempts that created these oversight rules. And so if you go back to - basically the CIA was founded in 1947, and at the time, there was concern that it's very hard to balance a secret intelligence organization inside an open democracy.

So they set the CIA up, and they specifically worried at the time that we did not want, in this country, to have something like the KGB or like the East German secret police. So they set boundaries, among which were that the CIA cannot operate in our own country.

Then in the 1970s, a number of abuses surfaced, and there became this, as you mentioned, the Church Committee, a congressional investigation that looked into allegations that the CIA was engaged in an assassination plot against Castro, one against an African leader, Lumumba. There were reports of interferences in elections in Latin America. There were reports about mind-control experiments with drugs on human beings that were being done, including one that resulted in a death of somebody jumping out of a window after having been given LSD without knowing about it.

There were also questions of illegal break-ins, including some into the private property of anti-war protestors in this country during the Vietnam War years, where the CIA assisted the FBI in particular in breaking into the psychiatric office of a doctor who was treating an anti-war protestor.

So these sorts of things became fodder for national scandal and outrage, and the result was an effort to try to reform the CIA. And the thought was that if Congress was authorized and required to perform an oversight role that there would be some checks and balances put in place on what the CIA was doing. It was very much a kind of mirroring what we do in other parts of the government, where you have outside, independent review in order to check abuses. And so that's how this - these oversight rules got set up in the first place.

DAVIES: Dick Cheney was a player back in the '70s. Remind us where he was and how this experience informed his own views, then and now, about the CIA and its relationship to congressional oversight.

Ms. MAYER: At the time, Vice President Cheney was the chief of staff to former President Gerald Ford, and so he was in the White House when some of these scandals were breaking, and he - from the time, and he's written about it, talked about it, he has looked at the Congress as having, you know, an illegitimate role here in trying to break the role that the executive branch, as he sees it, should play.

So he's described Congress as gnats in the past. And his top lawyer, David Addington, who actually was a lawyer at the CIA in the '80s, the two of them have worked hard to try to minimize the role of Congress and maximize the role of the executive branch.

So there's been this ongoing fight. And under Cheney's interpretation, I mean, he really feels that he needs to have a strong executive in order to have a strong America and that Congress shouldn't interfere.

DAVIES: Then there was the Iran-Contra affair, and Dick Cheney was in Congress at the time. Remind us briefly what that was about and what Cheney's views were then.

Ms. MAYER: Basically, this was when Reagan was president. Reagan wanted to fund the one side in the Nicaraguan civil war, and Congress explicitly forbade the White House from funding one side in the war. They didn't want to get involved in this, but the White House went ahead and did it anyway, along with the CIA. And what they did was they funded the Contras with money that was raised abroad instead of getting it out of Congress.

Congress was furious when they found out. There were all kinds of hearings, many legal repercussions, but throughout this whole thing, what was interesting is that Cheney always took the side of the White House, even though he was in Congress. He thought that it was up to the president to make foreign policy.

DAVIES: Now, apart from the battles of the 1970s changing the relationship between the CIA and Congress, it also changed the CIA and its conception of itself. And I'm wondering as somebody who follows the intelligence community, are you surprised to see a renewed interest in the CIA in developing, well, targeted killing squads?

Ms. MAYER: Well, I mean, I think you have to understand where this is coming from. It was right after 9/11, and the Bush White House was panicking about the possibility of another attack from al-Qaida. And they basically pulled out all the stops and decided they would do everything they could possibly think of, and the same with the CIA, which came the week after 9/11 - went over to the White House with a list of things that they would like to do, and this was on the list.

DAVIES: And you know, of course, there have been efforts to kill al-Qaida leaders going back through the 1990s, usually using guided missile strikes or drone aircraft. What's the difference between the military undertaking the killing of an al-Qaida operative and the CIA doing it?

Ms. MAYER: Well, the problem beneath all of this, it's very complicated, but the problem is, you know, whether or not you regard al-Qaida leaders as suspects in crimes or if they are warriors in a war. There's one set of laws that governs how we treat people in wars and another if they are criminals, and so there's been a lot of confusion about a sort of blurring the barriers there.

After 9/11, we basically went to war against al-Qaida. So the laws of war should have applied to the al-Qaida leaders here.

DAVIES: So then a military attack against an enemy of the United States is different from a killing of someone who is a suspected criminal. If the government views us as being at war with architects of terror, can the CIA be, in effect, employed as a military asset and conduct those killings around the world?

Ms. MAYER: Right. Conceivably, you can argue that they have the right to kill the enemy because we're at war with the enemy. And Congress wrote up the authorization to use military force, which gave the U.S. the power to go to war against the leaders of al-Qaida and the Taliban.

The question, though, is where's the battlefield? You can, under the rules of law, you can kill people, the enemy on the battlefield, but you can't necessarily chase them into sovereign states that are not part of this battle.

DAVIES: We're speaking with Jane Mayer. She's a staff writer for the New Yorker. We'll talk more after a break. This is FRESH AIR.

(Soundbite of music)

DAVIES: If you're just joining us, our guest is Jane Mayer. She is a staff writer for the New Yorker, where she's written on security and intelligence issues. She's also the author of the book, "The Dark Side: The Inside Story of How the War on Terror Turned Into a War on American Ideals."

You know, the battle that we're seeing now is not just about whether or not Congress should be briefed about some of these activities, but it really reflects this question of to what extent the Obama administration will now look back and hold Bush administration's accountable for alleged violations of law in its security activities, or in the interest of, you know, political compromise and national unity, let some of those things go and move on to a more forward-thinking agenda. Is this going to make it harder for Obama to confront that dilemma?

Ms. MAYER: Well, I mean, the problem is that from the start, you know, even before he was elected, Obama made a major issue of Bush's policies in the war on terror. He was an outspoken critic of them. So when he took over the White House, people expected him to end these policies and hold wrongdoers accountable. But he kind of instead, when he took over, said that we will fix what went wrong, but we don't want to look back. We want to look forward and not get caught up in punishing people who may have done wrong during these past years.

It's been a very hard line to walk, though, and it's getting harder all the time because there's more and more information suggesting there was serious wrongdoing of various sorts that took place during the Bush years.

DAVIES: And each time a new revelation emerges, he is called upon to comment and maybe confront a new decision about whether there should be an investigation.

Ms. MAYER: Absolutely. I mean, and so the thing is, he - the choice becomes does he want to open up the past, or does he want to cover up the past? And instead, he's looking for some kind of middle ground, where he can be neutral on this issue, not covering up necessarily for Bush but also not getting dragged into partisan fights about prosecuting his predecessors. And it's just - it's a swamp that he keeps getting dragged into.

DAVIES: And then there's this still-pending decision by the Attorney General Eric Holder on whether there will be investigations into those who developed the legal authority for enhanced interrogation techniques - torture. Now help us understand this. I believe the administration has said that they will not investigate or prosecute people who were acting within the legal limits that the Justice Department defined at the time. Is that right?

Ms. MAYER: Right. So basically they're trying to, you know, inoculate the CIA officers, who were acting in good faith and were told that what they were doing was legal, because it would seem unfair to go back at them now and change the rules on them. And so they have also said that - the Obama administration, that is - that they are not likely to prosecute the lawyers whose interpretations of the laws were so controversial.

So what's left, then, is the question - and it seems from recent reports that Attorney General Holder is looking at the possibility of appointing a special prosecutor who would investigate whether interrogators themselves, the people in the room with those terror suspects, whether they crossed over the line criminally, whether they went beyond even the very generous kinds of interpretations of law that the Justice Department during the Bush years gave them.

DAVIES: What might be the fallout from prosecuting those who actually inflicted torture?

Ms. MAYER: Well, I think the problem may be that the actual interrogators would argue immediately that they were authorized to do everything they did. And they would then point straight up the chain of command and say that the blame should be pushed upwards to the very top of the Bush administration, which after all signed off on this program, including the president, the vice president, the director of the CIA and the secretary of defense. So it wouldn't - it's very hard to contain this at the very bottom rungs of the program, and I think that's what they would find very quickly.

DAVIES: You know, with the revelations that have come out over the past, you know, days and weeks, do you think the balance has shifted in terms of the pressure on President Obama to more aggressively investigate alleged wrongdoing during the Bush days, or will he stay on the course that he has charted so far, to do as little as possible?

Ms. MAYER: You know, I just don't know that he can stay on this course. I understand very much why he wants to do it. This - you know, he doesn't want to tangle his presidency up in endlessly trying to deal with the problems that the former president created in the war on terror. And you know, clearly President Obama's got his own positive agenda. He wants to deal with health care. He wants to deal with the economy. The country probably agrees with his priorities in many ways, yet there is something about these legal problems that are coming out of the Bush years that you can't just sweep under the rug.

And I've been interviewing a number of experts on this area who say it's very much the experience that other countries have had when they've had scandals that involved allegations of torture. Frequently, everybody wants to just fix it and move on, but it doesn't go away - that these allegations are so serious, and they strike so much at the core of our values that people don't feel comfortable just letting perpetrators off the hook. And so it just keeps bubbling up and bubbling up until there's some kind of either a truth and reconciliation commission or some kinds of prosecutions or some way of just opening up what happened here because, you know, we're an open society, and torture is a major crime. So it's very hard to forget it.

DAVIES: You know, there are also international obligations, which may force the United States's hand in dealing with issues of torture, and we've seen efforts by a Spanish judge to bring some Bush administration officials to account. Where is that going to go? What impact will that have on the Obama administration's actions?

Ms. MAYER: Well, this is another problem for the administration because Eric Holder may not be free to ignore these allegations of torture. As you say, under international law, the convention against torture requires the United States to investigate if there are credible allegations of torture, and if we don't do it, other countries will, which creates a very uncomfortable situation, as we've seen in Spain, where they've started to take, you know, open up a criminal investigation into the U.S. So again, Holder may not be free to just move on without looking at this.

GROSS: Jane Mayer will continue her interview with FRESH AIR contributor Dave Davies in the second half of the show. Jane Mayer writes for the New Yorker magazine. Dave Davies is a senior writer for the Philadelphia Daily News. I'm Terry Gross, and this is FRESH AIR.

(Soundbite of music)

GROSS: This is FRESH AIR. I'm Terry Gross.

Leon Panetta just revealed to Congress that the CIA had a secret program to kill al-Qaida operatives, a program it kept hidden from Congress. Our guest, Jane Mayer, recently wrote a New Yorker article about Leon Panetta and what he faces as the new head of the CIA. Mayer is a staff writer for the magazine and is the author of the bestseller, "The Dark Side: The Inside Story of How the War on Terror Turned Into a War on American Ideals."

Let's get back to her interview with FRESH AIR contributor Dave Davies.

DAVIES: You wrote recently in The New Yorker about Leon Panetta and his efforts to reform the CIA and confront the dilemmas it faces about its recent past. One of the first things Panetta had to confront was whether he had an agency in which operatives under his command had committed torture. Is it clear whether that was the case?

Ms. JANE MAYER (Staff writer, The New Yorker): Well, the thing is it depends whose definition of torture? In the Bush years, the lawyers said that the things that were done in these interrogation programs were not torture. Many outside experts have said this clearly was torture, including the Red Cross, which is pretty much the world's expert on torture and war crimes. So there's a, you know, a fight on about whether what was done constitutes criminal actions or not. And you know, many people think that this was a program of torture.

DAVIES: Now, you tell us in the piece that when Leon Panetta came in he said he wanted to be sure that nobody on the CIA payroll could be prosecuted for torture or related crimes. How did he go about ensuring that that was the case?

Ms. MAYER: Well, he asked the inspector general, John Helgerson, at the time, whether Helgerson thought there were people there who had committed crimes and...

DAVIES: That's the inspector general of the CIA, right?

Ms. MAYER: That's right.

DAVIES: Right.

Ms. MAYER: And whether people needed to be investigated further there. And interestingly, Helgerson said he did not think there were - there were no people he knew of at the time who had committed crimes. But he also left the door open saying, you know, potentially more could be found out about people.

DAVIES: So where does that leave Panetta? I mean what standard did he employ?

Ms. MAYER: Panetta…

(Soundbite of laughter)

Ms. MAYER: Well, Panetta's in a tough spot. He wants to win over the loyalty of the building. He doesn't want to alienate the people who's, you know, who he is the boss of. And so he pretty much has decided to take the same line as President Obama saying, if these acts were authorized by lawyers in the Bush administration, then he doesn't think people should be prosecuted now that we're reinterpreting the law. So he seems to be, you know, to some extent accepting what was done before and trying to move forward.

DAVIES: Now one of the things that President Obama has said is there's going to be a new era of openness and transparency. To what extent has Panetta done that or maybe been more protective of the CIA when it comes to the disclosure of past deeds and memoranda reports?

Ms. MAYER: Well, he has kind of moved back and forth on this, taking something of a middle course. I mean he has released a number of documents, including almost all of the legal memos that the Justice Department wrote during the Bush years that guided this program, some of which have been filled with absolutely shocking details. So that was transparent to some extent. But he also has obviously held back on a number of things when he's been advised that it will hurt national security.

So, for instance, he didn't release the photographs of detainees being tormented in various ways recently because he was afraid that it might stir up some kind of anti-American backlash. And there are other areas where his Justice Department has asserted national security rather than opening up secrets. And there have been a number of critics saying that they think he's -that Obama has been too much like Bush in over-asserting national security secrets.

DAVIES: Panetta at the CIA also had to deal with this issue of rendition, of taking prisoners and then having them transported to countries where they might undergo torture or really intensive interrogation techniques. Where has Panetta come down on the rendition program?

Ms. MAYER: Well, it's interesting, and I think surprising to many critics of rendition that Panetta and the Obama administration are continuing the rendition program, which they say they're going to do differently than the Bush administration did. In the Bush years this program just grew exponentially and resulted in a number of allegations. The people who the CIA picked up and basically abducted and sent over to foreign prisons to be interrogated, many of those people allege that they were hideously tortured.

So what Panetta told me was that they're going to monitor it much more closely and they're going to make sure that nobody gets sent to a country where they torture or abuse prisoners, and that they - we will keep tabs on them to make sure that they are treated humanely. Which sounds good, but it is actually what the Bush administration said too.

This is a program, to be honest, that began during the Clinton years. And so it - and there are a number of people inside the CIA who think that it's very effective, so they've been pushing Panetta and Obama to keep it going.

DAVIES: How credible do you find these assurances that people can be protected?

Ms. MAYER: I think it's very hard. I mean there are very few countries that live up to the United States' standards of justice. So, I mean, even during the Clinton years they - the CIA picked up a number of suspects and sent them to Egypt and some of them were summarily executed. So it's very hard to say that you can find other countries...

(Soundbite of laughter)

Ms. MAYER: ...that live up to our standards of human rights. And I mean I think it's, you know, it's asking for trouble, I think.

DAVIES: What's the logic of maintaining a rendition program? Isn't it designed to evade protections in U.S. law? Why would the United States government want to do that?

Ms. MAYER: Well, actually there are many people who think the rendition program is very effective. It's not necessarily just designed to evade U.S. law. What it's designed to do is pick up terror suspects around the world and capture them and deliver them into some form of justice, if not our own, and some have been brought to our country, but then to some other countries, an allied country that maybe will be able to prosecute these people. So some of them are taken to the countries that, you know, where they are citizens. And we're just sort of assisting other countries in bringing people to justice.

I mean, in theory I can see why it has an appeal because, you know, it picks people up off the street who might be extremely dangerous terror suspects. But the question is whether the U.S. should be involved in bringing people into circumstances where they might be tortured and we have laws that say we can't bring them to places that'll torture them. And then the question is, well, can we monitor this appropriately, and it's hard to do.

DAVIES: You know it's interesting that Panetta's dilemma at the CIA is sort of parallel to Obama's, but they're different. I mean, Obama has to make a decision that's to some extent a political calculation. Whether it's better for the country to honestly confront its past or to let some of that go unexamined so that he can build a national consensus to move forward on an important agenda, everything from health care to the economy to energy.

Panetta has a managerial challenge. I mean he needs to get his agency moving on a very important national security mission that might be undermined if he spends a long time going into investigations and recriminations on past deeds. And I'm wondering what your sense is of the extent to which Panetta's goals for the CIA, and obviously it does a lot more than interrogate people, to what extent his goals for the agency have been undermined by, you know, the looks -the investigation of its past?

Ms. MAYER: Well, I think there is a great fear that he and others have over at the CIA that if they start opening criminal investigations or even disciplinary investigations into the counterterrorism staff that it will hurt the morale of the agency and make the - particularly tie up the time of the experts in counterterrorism at a time when we still face a threat from terrorism.

(Soundbite of laughter)

Ms. MAYER: So it is a real dilemma. Though I have to say that, and it's very much also what the Republicans on the Hill have been saying. They've been arguing that this is a dangerous course to take and it's going to weaken the CIA if you hold people accountable for past abuse. It's - one of the things that intrigues me about this argument though is that the military, of course, does this all the time. If there are allegations of war crimes they investigate them.

If, you know, obviously in Abu Ghraib a number of people were charged with crimes. And what they - part of the reason they do that is to keep high standards of discipline and also to learn lessons from things they did wrong in the past. And I think, you know, weighing on the other side of this argument is the question of whether the CIA has learned something from this period. Have they really decided that abuse is - was unnecessary and wrong and off the table? Or would we possibly slip back into this if there was another attack? And I think it's very unclear. So there's kind of a lot of confusion over...

(Soundbite of laughter)

Ms. MAYER: ...over at the agency and it's up to Panetta to try to straighten all of this out.

DAVIES: Well, Jane Mayer, thanks so much for joining us again.

Ms. MAYER: Glad to be with you.

GROSS: Jane Mayer speaking with FRESH AIR contributor Dave Davies. Mayer writes for The New Yorker and is the author of "The Dark Side." Dave is a senior writer for the Philadelphia Daily News.

This is FRESH AIR.

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