In our interview, Brennan discussed restructuring the intelligence community, renewing FISA and debating counterterrorism on the campaign trail. Edited excerpts follow. You can also access the transcript at National Journal’s Web site.

Q: Are we hearing a sufficient level of debate and distinction among the candidates of their various national security and counterterrorism positions?

Brennan: I think we are hearing some of that debate. And that debate is going to intensify as we get closer to the election.

There has been a fair amount of discussion, particularly on the terrorism front, about the different types of approaches. But I think it’s mainly at the strategic level.

The intelligence business is a very complicated one, and I think a lot of the nuances may be lost on people. It’s difficult in a presidential debate to really get into those intricacies.

I think there’s a real issue related to some of the approaches that the next administration will have toward some of those countries, in particular, that still pose national security challenges to us — for example, Iran, and whether or not there needs to be some initiative on the part of the United States to see whether there’s some way to bridge the gap, or whether we should maintain a confrontational posture toward Iran.

Senator Obama and Senator [Hillary Rodham] Clinton have expressed an interest in trying to reach out, even to our adversaries. There are differences between those two as to when the president should get engaged.

Q: As a counterterrorism professional, is there one path that you see as more productive?

Brennan: I think that what we need in our quiver are many different types of arrows. We certainly need to have a military arrow. We need to have an intelligence one. But we need to have a diplomatic one. We need to have foreign aid. There needs to be a comprehensive set of approaches. A lot of these issues, including counterterrorism, cannot be solved with kinetic force.

I am a strong proponent of trying to focus more of our efforts on the upstream phenomenon of terrorism. I make the analogy to pollution. We learned that pollutants kill us when they get into the water we drink or the fish we eat or the air we breathe. But I think we also learned that we have to go upstream to identify and eliminate those sources of pollution. Terrorism is a tactic, and we have to be more focused upstream. Since 9/11, understandably we’ve focused downstream, on those terrorists who might be in our midst or trying to kill us, the operators. I think there needs to be much more attention paid to those upstream factors and conditions that spawn terrorists.

We also have to have a full discussion about the appropriate techniques we’re going to use when individuals are captured or detained. But we have to be looking at what are those foreign policies, aid programs, international efforts that we need to be engaged in, that are going to try and stem the flow of those terrorists further upstream. I think a lot of our resources have been dedicated to that downstream phenomenon; I think the United States is a lot safer because we put in place the security filters to prevent terrorists from coming into our country. Now we have to look at the longer-term issues that are more difficult to deal with — why individuals are succumbing to a lot of the recruitment efforts on the part of terrorist groups.

Q: What is the appropriate government agency to handle that?

Brennan: This is an issue the government is grappling with. A lot of the issues right now fall between the Department of State and the Department of Defense and Commerce and others. I think as we deal with these transnational issues, we need to bring to bear those capabilities that exist in different agencies. The National Counterterrorism Center is a place that is trying to deal with the issue in a comprehensive fashion. They have a group there, the Strategic Operational Planning Group, which is trying to bring to bear the full instruments of U.S. national power, from the diplomatic front to the intelligence front to law enforcement and defense. I think we need to have more of these integrated efforts, because no single department can in fact address the issues.

Q: People like you have talked about the need to do this for some time. Why haven’t we seen this take hold as an ethos in government?

Brennan: There are a number of factors. One is, it’s really, really hard. It addresses legacy institutions and architectures and ways of doing business. In Washington, it’s difficult to rearrange how you do work. It would be overhauling, in many respects, the way we do government work. That requires legislation, a close interaction and coordination between the executive and legislative branches, and it also affects a lot of rice bowls.

Q: Then what will it take to finally push this through and make agencies feel compelled to change?

Brennan: It certainly isn’t something that should be done quickly or without appropriate thought. I’m an advocate of having a review of the U.S. governance structures that’s going to transcend administrations. It’s going to be something that people are going to get together and say, “What type of governance structures and changes need to take place so that we can deal with the challenges of 2015, 2020?” The Department of Defense went though the Goldwater-Nichols Act [which changed the military command structure], but I would argue reorganizing a department is easier than reorganizing how many agencies are going to interoperate. I think we still are struggling with that.

Q: Would it make sense then to make the Director of National Intelligence more like the FBI director, someone who’s not necessarily going to leave when the administration changes?

Brennan: I’m an advocate of having term appointments for the Director of National Intelligence. I think it makes sense. But the intelligence community is a subset of the broader national security establishment, which is a subset of the broader U.S. government. I would argue that the challenge for the next decade is how you’re going to ensure better interaction between the federal, state, and local elements, in terms of information sharing, knowledge, and expertise.

Q: In your estimation, where is the threat level of terrorism today versus where it was right after 9/11? How big is the threat domestically? How has it changed?

Brennan: There are two sides to that coin. Whenever you do a net assessment, you look at the threat and the vulnerability. Let me take the vulnerability side. A lot has happened in the past six years in terms of making the homeland a much less hospitable environment for terrorists to ply their trade. We should feel good that our borders are not as porous. There’s a much more substantial watch-listing effort. And a much better capability to detect terrorists and terrorist activity within our borders.

That said, on the threat side, while Al Qaeda, the organization, has been badly bloodied since 9/11, they still retain a potentially lethal capability. There has been a metastasis. Al Qaeda has manifested itself in a lot of different countries and communities, and it’s a movement that continues to be grown and fueled by a number of factors.

One, is, since the collapse of the Soviet Union, we no longer have this bipolar world where you had the United States and the Soviet Union competing with each other and proxies lining up behind them. We now have basically a unilateral world with the United States as the sole superpower from a military and economic standpoint. But also, we’ve seen the fading away of a lot of competing ideologies: socialism, Baathism, Nasserism, communism and others. They have been discredited. You have in some respects Western capitalism on one side, and on the other side, maybe those religiously-driven forms of extremism. Islamic extremism has filled the void where in the past there were alternatives in terms of competing ideologies. We don’t have the same number of “-isms” out there. And so I think this [Islamic extremism] is going to continue to garner support and recruits in different parts of the world.

Q: Compare our ability to counter ideologies versus our tactical capabilities to collect more intelligence, to share it, to do more sophisticated things with it.

Brennan: I think unfortunately we have been way behind the curve as far as the public relations campaign — making sure the image of the United States is seen in a more positive light. When I first went to the Middle East, I studied in Cairo in 1975, and the U.S. was viewed as the sponsor and supporter of Israel. But when I was in Egypt, I was regularly befriended by people, because Americans were still looked upon in a very positive way. Unfortunately, the U.S. image now is not the same as it was several decades ago. The Iraq situation, unfortunately, was viewed as military adventurism on the part of the United States. We need to repair that image. We need to make sure we convey to the world the types of things the United States is committed to. That is very difficult. Focusing on the downstream effort is, in some respects, easier because it’s more tangible. You can go after those high-value targets; you can go after those training camps.

Q: In the 2004 campaign, it seemed you had on one hand President Bush talking about downstream efforts, and then John Kerry articulating something more like the public diplomacy approach. It became a partisan division: that if you were for public diplomacy, you were weaker and identified with Democrats, and if you were on the Republican side, then you were with the president and fighting the fight. It seems not that pronounced this time, and that the candidates are talking more about combating ideologies. Is there still a divide between hard war and soft war?

Brennan: I think there is a divide. Obama is a good example in terms of the different approaches between the parties. In the articulation of the public effort, there needs to be the companion discussion about the need to act forcefully to ensure that U.S. lives and property are protected. I think some of the statement you see coming out from the Democratic side is to reassure the American public that although public diplomacy is going to be a major part of that foreign policy approach, it’s not going to be at the expense of ensuring that we’re going to be able to utilize military and other measures to take action against the threats.

Q: Assess the debate in Congress and with the administration over reforming the Foreign Intelligence Surveillance Act. [Democratic lawmakers allowed the temporary extension of that law, the Protect America Act, to expire, over the vehement objections of the White House.] Why has it come to this point where politics has arguably pulled things off the rails?

Brennan: There is this great debate over whether or not the telecom companies should in fact be given immunity for their agreement to provide support and cooperate with the government after 9/11. I do believe strongly that they should be granted that immunity, because they were told to do so by the appropriate authorities that were operating in a legal context, and so I think that’s important. And I know people are concerned about that, but I do believe that’s the right thing to do. I do believe the Senate version of the FISA bill addresses the issues appropriately. [Director of National Intelligence] Mike McConnell, I think, did a very good job trying to articulate the distinctions between the old FISA law, the FISA understanding under the Protect America Act, and then the House and Senate versions.

There are many types of scenarios for signals [for example, telephone calls and e-mails] to be accessed. But whenever this happens, there needs to be some substantive predicate, a probable cause, that someone is being targeted appropriately. There is an important issue about timeliness. And even though you can go through the FISA process, particularly when you’re dealing with terrorism issues, there needs to be an understanding that intelligence agencies can move quickly if certain predicates are met. We shouldn’t be held hostage to a complicated, globalized [information technology] structure that puts up obstacles to that timely collection. I think there are some very, very sensible people on both sides of the partisan divide trying to make this happen. And it’s unfortunate that it’s become embroiled now in a partisan debate in some quarters. But I think that’s expected in any election year, especially one like this.

Q: So how do we get to the point where the public has reasonable assurances that what an intelligence agency does to determine probable cause, or that predicate, is based on sound technique?

Brennan: Maybe there needs to be a system of executive, legislative and judicial representatives who are going to oversee and ensure that this moves along the right path. It really takes those three legs of government to make sure there aren’t advertent or inadvertent abuses.

You can have FISA judges and representatives from Congress, not to routinely review those individual requests [for surveillance], but the process, the criteria, and to make sure it’s being followed in a strict fashion.

Q: You know that one big debate about FISA is the question of balancing security and privacy and civil liberties. Speaking as someone who has spent your life in counterterrorism, what do the terms “privacy” and “civil liberties” mean to you, and what is that balance?

Brennan: First of all, privacy and civil liberties mean so many different things to different people. There are people on one end of the spectrum that don’t want to have any government interference or insight into what you’re doing.

To me, I think the government does have the right and the obligation to ensure the security and safety of its citizens. If there is probable cause, reasonable suspicion, about the involvement of a U.S. person in something, the government needs to have the ability to understand what the nature of that involvement is. The threshold for that type of government access can be high or can be low, and it needs to be somewhere in the middle.

It really gets back to that issue of what is the substantive predicate. … If we know there’s a terrorist overseas that has been involved in activities, but he’s also an import-export dealer, and he reaches out to Shane Harris because you happen to be an importer of stuff — you’re a U.S. citizen — and we can see there’s contact going on there, well, is that sufficient to give us reasonable suspicion that Shane Harris is involved in something? And Shane Harris happens to be in touch with somebody in his neighborhood that has a past record in engagement in some type of things. So there is going to be a judgment call here.

And what I think is important is that there needs to be an airing of this issue, public hearings that Congress can hold. You can’t explain the issue in such rich detail that you can say exactly where that line is going to be drawn. But there needs to be an articulation of those triggers that the American people overall feel, yes, that’s the right thing for the government to do.

You don’t want to just troll and with a large net just pull up everything. There are technologies available to pulse the data set and pull back only that which has some type of correlation to your predicate.

Q: Is this the difference between the government controlling information, locking it down, and having controlled access to certain data sets which do exist?

Brennan: Right. And I would argue for the latter. Private sector companies can do things the government is unable to do, for marketing to their clients. I would argue the government needs to have access to only those nuggets of information that have some kind of predicate. That way the government can touch it and pull back only that which is related. It’s like a magnet, set to a certain calibration. That’s what I think we need to go to.

In the immediate aftermath of 9/11, the threshold, quite frankly, was low, because we didn’t know the nature of the threat we faced here in the U.S. Every effort was made by the government to try to get as much understanding and visibility into what else might be out there that’s going to hurt us again. Now that a number of years have passed, we need to make sure the calibration is important. But maybe in a period of heightened threat you have to recalibrate that based on new information you have — new intelligence that’s going to give you a better sense of where to aim your magnet.

These are things that need to be discussed openly — not to the point of revealing sources and methods and giving the potential terrorists out there insight into our capability — but to make sure there is a general understanding and consensus that these initiatives, collections, capabilities, and techniques comport with American values and are appropriately adjusted to deal with the threat we face.

Q: How does the next president go about doing that?

Brennan: It’s going to be a real tough job. Even though people may criticize what has happened during the two Bush administrations, there has been a fair amount of continuity. A new administration, be it Republican or Democrat — you’re going to have a fairly significant change of people involved at the senior-most levels. And I would argue for continuity in those early stages.

You don’t want to whipsaw the [intelligence] community. You don’t want to presume knowledge about how things fit together and why things are being done the way they are being done. And you have to understand the implication, then, of making any major changes or redirecting things. I’m hoping there will be a number of professionals coming in who have an understanding of the evolution of the capabilities in the community over the past six years, because there is a method to how things have changed and adapted. My advice, to whoever is coming in, is they need to spend some time learning, understanding what’s out there, inventorying those things, and identifying those key issues or priorities that they have — FISA or something else. They need to make sure they do their homework, and it’s not just going to be knee-jerk responses.

Q: In other words, don’t come in and do a housecleaning?

Brennan: Right — not just in terms of people, but also programs. You don’t want to create upheaval, because it will create a disruption in the system. There are still a lot people who say we have to implement all of the recommendations of the 9/11 Commission. I have problems with some of those, because they’re not really anchored in reality. Sometimes a superficial understanding of a problem leads one to making superficial decisions.

Q: It seems unlikely that any of the leading candidates would come in and dismantle things. They’re fairly savvy to the kinds of things you’re talking about. Is that the case, or is there still a risk there will be a political calculation, in that the next president will need to make a demonstrable effort to wipe the slate?

Brennan: I don’t think anybody’s going to come in and just make wholesale changes. But there’s going to be a learning curve… at a time when you’re still faced with national security challenges. So they have to be learning as they go, but at the same time managing all these issues and making sure they don’t drop any balls at all. It’s going to be challenging, and I wouldn’t be surprised if some of America’s enemies didn’t see if they could take advantage of that transition, and to see whether or not they can do things that are going to be confrontational and provocative to test the new administration.

Published in National Journal.

Who is out there actually defending the NIE? Israel now joins the French, the President of the United States, and the U.S. Director of National Intelligence in concluding that Iran is still on the path to a nuke, despite the NIE’s judgment that Iran halted its nuclear weaponization program years ago. Like the other NIE skeptics, Israel homes in on two key pillars of a nuclear program, including uranium enrichment and ballistic missile construction, and concludes that Iran’s nuclear ambitions are alive and thriving. (President Bush made this case publicly, as well.)

Israel’s departure with the NIE differed in that it rebuked the document itself as diplomatically counterproductive, something that, so far, only staunch critics of the intelligence community in the United States have done. Israel’s reaction is hardly surprising, of course, given its particularly precarious position in the region, and its long-standing insistence that Iran is either close or very close to developing a nuclear weapon.

But the fact that Israel is now on record against the U.S. conclusion is an important development, and could signal the start of a new international alliance, backed by President Bush himself, against the NIE’s conclusion, which will continue to be painted as rosy, overly optimistic, and fundamentally off-the-mark because it doesn’t rank the enrichment and missile programs highly enough in the final calculation. Will the authors of the NIE defend their work again, as they did so forcefully when their key judgments were declassified late last year? Stay tuned.

In the meantime, here’s something from the vault on Israel’s historic insistence that Iran was practically within reach of a nuke. In October 2006, I sat in on a meeting between then-Congressman Curt Weldon, a Pennsylvania Republican, and Daniel Ayalon, then Israel’s ambassador to the United States. (I was writing a profile of Weldon, and the two men had previously scheduled this meeting in Weldon’s office.) The conversation turned to Iran’s nuclear ambitions, a topic that had possessed Weldon’s interest. Like the Israelis, he insisted that Iran was closer to a weapon than most people thought, and that the United States perilously underestimated the regime.

Weldon told Ayalon that Iran would have a nuclear weapon in two years. A military attaché who had accompanied Ayalon to the meeting replied, with a smile, “We say less.” It was a chilling moment, in and of itself. But it also stood out because, at the time, such a dire assessment was at odds with most experts’ opinion, as well as the judgment of the CIA and other U.S. intelligence agencies. They estimated then that Iran’s weapons program was at least five years from maturity and probably more, given Iran’s difficulty producing the necessary materials for a bomb. It’s worth noting that, around the time of this meeting, the intelligence community would have been in the early stages of its reassessment of the Iranian program, which resulted in last year’s NIE and the about-face on the previous assessment.

A nascent and evolving theory is that the administration is signaling now, to Pakistani President Pervez Musharraf and the world, that the United States is more prepared than it has been in years to send American forces into Pakistan’s lawless tribal areas to do what Musharraf either cannot or will not–rout the resurgent Al Qaeda.

Consider some of the key plot points that have led to the current moment in the Pakistan narrative. In February, Defense Secretary Robert Gates made a surprise visit to Pakistan, ostensibly to ease the “war of words” between that country and Afghanistan over what to do with the troubled tribal areas. But Gates was also there to deliver a message to Musharraf–you need to do more to fix this problem.

About two weeks later, Vice President Dick Cheney flew to Islamabad to meet with Musharraf, taking with him the CIA’s deputy director, Stephen Kappes, an seasoned spy and longtime Asia hand who had served in Pakistan. This was not a cordial call. Musharraf’s intelligence services were, and still are, in shambles. Officials don’t know who is loyal to Musharraf and who is loyal to jihadits in Pakistan, and this limits their effectiveness. Musharraf clearly lacks the human intelligence to get close to Al Qaeda without seeing his own troops slaughtered. So, one has to conclude that Kappes was there to provide the Pakistani president with more than moral support. The CIA is giving him intelligence, likely helping him understand who in his own country is trying to kill him, and to help Musharraf deal with the tribal areas. (Apparently this strategy hasn’t been terribly effective, if the intelligence community’s own judgment is that Al Qaeda is strong again.)

At the same time Cheney and Kappes were meeting with Musharraf, senior intelligence officials were briefing reporters on the growing threat of Al Qaeda in Pakistan, telling them that the organization had replenished its middle ranks. Intelligence indicated that the foiled British planes bombing plot the previous year had an operational link to the resurgent group, they said.

Fast forward to this month. The New York Times reported that, in 2005, the Pentagon called off a clandestine U.S. strike in the tribal areas aimed at capturing Al Qaeda officials. Then Defense Secretary Donald Rumsfeld worried that the strike–which apparently had ballooned into a full-fledged invasion when military planners demanded security cover–would jeopardize U.S.-Pakistan relations. But in leaking this story two years later, the message to Musharraf from the Pentagon and the intelligence community was clear: We hesitated then, we won’t now.

That brings us to this week’s NIE, which put the official stamp on what we’ve known for months. A few days before its release, the intelligence community’s top analyst publicly briefed members of Congress on the substance of the Pakistan problem.

Taken together, this build-up in U.S. anxiety–first expressed in surprise visits by top officials, now playing out in congressional testimony and public intelligence documents–signals that the Bush administration is dispensing with its light-touch strategy. It was that approach that kept thousands of combat troops from descending into the tribal areas in 2005. This has been replaced by tough public rhetoric and an undercurrent of hostility.

One has to wonder if the administration thinks the time for words has past. Is the United States moving towards its own military solution to Al Qaeda in Pakistan? The administration has stayed off that course for fear it would so badly destabilize Musharraf that he would lose his grip on power, with disastrous consequences for American interests. Well, the country appears to be sliding into instability, so perhaps one objection has gone away. But if Al Qaeda really has re-charged its batteries, and is more capable of striking out from Pakistan today than it has been in years–which is now the official line–then the administration might think it has no choice but to strike, if Musharraf won’t.

It sounds implausible given the administration’s cautious strategy to date. But consider what would happen if an Al Qaeda cell linked to Pakistan mounts a devastating attack in the United States. The United States would respond with full force, a la Afghanistan in 2002. Is the administration prepared to wait for that moment? I think that you can read between lines of the past several months and conclude, “Probably not.”