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The tasks before Barack Obama’s new national security team are huge: execute the pullout of U.S. troops from Iraq, bring Afghanistan back from the brink, and open what the president-elect has called a “new dawn of American leadership” in the world. Few know these challenges better than James L. Jones, a former NATO commander and Marine general who has been tapped as the next U.S. national security advisor. In addition to his on-the-ground experience, General Jones has—for the last two years—been part of a “guiding coalition” for the Project on National Security Reform, whose new report recommends sweeping reforms to the U.S. national security apparatus.

The Project’s findings are brutally frank: The system is deeply flawed, inefficient, and poorly coordinated. There is waste and misallocation. James R. Locher III, the project’s executive director and a former assistant secretary of defense, told Foreign Policy’s Elizabeth Dickinson that national security reform is the “number one security issue” facing the United States today. Locher’s report offers a unique window into how General Jones and former Deputy National Security Advisor James B. Steinberg, another past commission member who is widely expected to land a top administration job, might approach the mission ahead of them.

Foreign Policy: In your preliminary findings, you describe today’s world as an unpredictable place—filled with non-traditional combat, resource competition, and rapidly changing circumstances. Can you give us a picture of that world from a security point of view?

James R. Locher III: The United States used to have one major enemy that we focused on. Now, [we face a] whole range of different threats and challenges. When we had to do multi-agency things [during the Cold War],for example, the Vietnam War, we struggled a long period of time figuring out how to integrate all the instruments of power. Now the world is a whole series of Vietnam-type events. We also still have to worry about various state actors.

These situations are incredibly complex and they’re changing very rapidly, which requires that we work horizontally across the government. I often like to use the example of the Global War on Terror. It’s a law enforcement issue, so we need the Department of Justice. We’re working with lots of countries and through the United Nations, so we need the Department of State. You have the Defense Department involved in the killing or capturing of terrorists. You need almost all elements of the intelligence community. We have Treasury involved because we’re trying to stem the flow of terrorist finances. Transportation is involved because that’s where terrorists like to strike—transportation networks. We have Health and Human Services involved because we’re worried about biological and chemical warfare. Then you have the Department of Homeland Security that worries about the domestic terrorist threat.

You need to integrate all that expertise and capability, and our government does not have the mechanisms to do that. The National Security Council are headquarters without headquarter powers. They are advisory only. The setbacks that we’ve had recently—from 9/11 to the trouble stability of the operations in Iraq and Afghanistan and the failed response to Hurricane Katrina—they’re all evidence of this misalignment of our government with the challenges we’re facing.

FP: In the case studies discussed in this report, you look at some of the crucial moments in U.S. national security, such as the decision to invade Iraq and the handling of the crisis in Somalia in the early 1990s. Are there underlying threads of weaknesses throughout these examples?

JR: Somalia was really a policy formulation problem. How do we formulate effective policy when we have a weak integrating mechanism and we have very powerful departments who hold on to their perspectives for a long period of time? The people on the ground in Somalia did not have a clear understanding, there was not an understanding in Washington as to what the situation was on the ground, and it lead to disastrous results.

With respect to the decision to invade Iraq—we did not have a very effective policy formulation. One of the first things that you have to do if you are going to have effective policy is you have to have a really rigorous assessment. That process did not occur.

FP: Was that a systematic failing, or was that more a problem of particular people who happened to be working on it?

JL: You always have the issue of personality; you never really get rid of it. And there were lots of personality issues at play there—key people who were allied on issues and who were incredibly powerful. You didn’t have that objective, hard-nosed analysis that you might like to have. But the system isn’t well designed in that regard. It can produce good policy on occasion—but it can lead to lowest common denominator or lots of stalemates or working outside of the system.