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LAURA SULLIVAN, HOST:

It's WEEKENDS on ALL THINGS CONSIDERED from NPR News. I'm Laura Sullivan. After 9/11, there was one man the American public wanted captured, Osama bin Laden. But there was a secret hunt going on for someone else, the real mastermind of the attacks.

JOSH MEYER: If Khalid Sheikh Mohammed had been taken off the battlefield or captured when the authorities had a chance to do that in the mid-'90s, there simply would have not been a 9/11 attack.

SULLIVAN: That's Josh Meyer. And along with Harry McDermott, he coauthored a book called "The Hunt for KSM: Inside the Pursuit and Takedown of the real 9/11 Mastermind, Khalid Sheikh Mohammed."

This week, the Department of Defense filed charges against KSM who has been held at Guantanamo since 2006. He's accused of being responsible for the deaths of 2,970 people and will stand trial before a military tribunal at Guantanamo Bay. As he was researching his book, Josh Meyer found Khalid Sheikh Mohammed complex and surprising.

MEYER: He's quite a fascinating individual. He's incredibly charismatic. He's extremely intelligent. He is able to meet people and get them to do things like, you know, blow themselves up for the cause within a matter of, you know, days or weeks. I mean, he's got this almost Svengali effect on people. He's also kind of a jokester and a prankster. He likes to crack jokes. I mean, in Guantanamo, he would make jokes at one point. But then, he would, all of the sudden, have this Charles Manson-like stare.

I mean, he's a very complicated guy. Even when he was on the run, they found a suitcase with all of his belongings, and it showed a lot of photos of him playing with his young children. So in some ways, he was a very doting family man.

SULLIVAN: A few people may realize that he actually attended college here in the United States. How did that experience go for him?

MEYER: Yeah. I mean, he got an engineering degree from North Carolina Agricultural and Technical, and I think that's one of the reasons he had such a chip on his shoulder against the United States. He encountered pretty serious discrimination. There were some guys at the college who liked to put, you know, like a pail of water on the door so then when he opened it, it spilled into the room. I mean, I think that he came back from that experience thinking that the United States was evil.

But I also think that it went far beyond that. I think that he was really fixated on what he thought were problems in American foreign policy. He was much more political than bin Laden and these other guys. I mean, he was religious too. But, you know, he hung around in karaoke bars, he drank alcohol, he, you know, picked up dancing girls in the Philippines. So he was not your typical jihadist.

SULLIVAN: But for a long time, the U.S. intelligence community had no idea - from your book - that this was even the guy that they were after. They had heard rumors and whispers of some guy named Muktar, which I guess means the head...

MEYER: Right. The brain or the chosen one.

SULLIVAN: ...or the chosen one.

MEYER: Yeah, right.

SULLIVAN: Why did it take them so long to figure out, even after the fact that this was the guy?

MEYER: It wasn't that they didn't know who KSM was. There was a small group of people, mostly the FBI agents from the New York field office, who were tracking KSM from 1993 well into 2003. The big problem was they didn't connect him to al-Qaida until 2002.

SULLIVAN: Wow. You called him a ghost.

MEYER: Right. And then once they connected him to 9/11, everybody said: Oh, my God. This guy that's been on our radar for so long is actually the guy that did 9/11. And that was just a complete panic moment. I mean, it basically rang all the way up to White House immediately. Satellites were retasked to try to find this guy, and it essentially was a redeployment of the whole war on terror.

SULLIVAN: It was just an all-out manhunt for him.

MEYER: Right. Right. But it was in secret. And that's what intrigued me for so long, was while bin Laden was in the headlines every day and there were military people, you know, soldiers looking for him and bombing Afghanistan, the hunt for KSM was a guns-drawn chase through the streets of places like Karachi by law enforcement, and it was in - kept in secret for many, many months.

SULLIVAN: Why did they do that? I mean, the public, we all sort of understood that Osama bin Laden was the guy we were after, that this is who we were chasing in caves and Afghanistan.

MEYER: Right.

SULLIVAN: In your book, you describe in such detail that who we were really chasing at that time was Khalid Sheikh Mohammed. Why would they keep that a secret? Why was that important to do that?

MEYER: They say it was because they wanted to have the element of surprise to catch him. But they didn't catch him. There were a group of agents from the FBI field office who went to as many as 30 countries over eight years looking for him, and they came close to catching him a few times. But every time, he was one step ahead of them and he got away.

SULLIVAN: I'm speaking with Josh Meyer about the book he coauthored called "The Hunt for KSM: Inside the Pursuit and Takedown of the Real 9/11 Mastermind, Khalid Sheikh Mohammed." Josh, your book shows so much that the CIA and the FBI does right, just such moments of just amazing work. And then there are moments where you just think this could not have gone any worse for an agency.

MEYER: Right. I think that one of the fundamental disconnects, which, you know, continues to this day, is that the CIA and the FBI essentially have competing agendas. One is to gather intelligence and prevent future attacks, the other is to gather evidence to be presented in a court of law and make criminal cases against people. And those two just don't mix.

SULLIVAN: And both the CIA and the FBI had these incredible missed opportunities to have prevented 9/11 from happening.

MEYER: Well, I mean, I think that the one thing that's the most important takeaway from this is that the small group of people that were hunting him, in some ways, were real, true American heroes. You had a guy named Frank Pellegrino, who was a former accountant and a lawyer who was a very idiosyncratic FBI agent. And he realized the dangers of KSM early on. He had a lot of trouble finding other FBI agents to work with him on this because, you know, it was hard work, it was a lot of international travel. And to get promoted in the FBI, you're basically promoted on the number of arrests you make and cases you make, and that doesn't happen in terrorism.

So he looked around, and he found a guy who was assigned to the Joint Terrorism Task Force who was a Port Authority cop named Matt Bashir, and then these two guys basically traveled the world together. And they basically gave up their lives, you know, their family life and so on, and spent most of their time overseas hunting KSM.

The problem was that after a while, the FBI New York office, FBI headquarters, the Justice Department, started thinking, well, you guys are spending way too much time looking for this one guy. I mean, you know, how dangerous can he be? So they were actually criticized and undermined for not participating in what was believed to be the most important trip, which was al-Qaida, when it turns out that the guy they were chasing was the guy who did 9/11. So there's an irony there that's rather unfortunate.

SULLIVAN: How did he end up getting caught?

MEYER: KSM was finally captured through a combination of methods. Some of them are still very secret. A lot of it was just shoe-leather detective work. They would catch one person and get some information that would lead to another person. But one of the big successes in the catch for KSM was that they developed an informant who was a Balochi, from the same part of Balochistan that KSM was from, and he was in KSM's orbit of people that he knew and trusted, and they were able to insert this person into KSM's circle of trusted confidantes.

And at one point, he was able to set up a meeting with KSM. And so while they were in a meeting, he goes to the bathroom, and he texts: I am with KSM, and that's how they knew that he was with him. Then they waited until the meeting was over, and then they took some other measures, which are classified, and then they captured KSM. And in the end, even though this was the most traumatic law enforcement manhunt probably in history, spanning 18 months even after 9/11, KSM was captured in his sleep.

SULLIVAN: Why did Khalid Sheikh Mohammed do it?

MEYER: He would be happy to tell you that. And I think that if he's given a chance in the upcoming trial, he'll do that. I mean, he is very open about his grievances. He thinks of himself as the equivalent of George Washington, the commanding general of an insurgent army fighting the British. I mean, he really believes that he is the good guy in all this and that he's fighting a war to protect Muslims from a U.S. government that he believes is propping up corrupt dictators around the world and launching wars that kill innocent people. So, he's got a very articulated position on this, and he really does believe that he's the good guy and we're the bad guys.

SULLIVAN: That's Josh Meyer. Along with Terry McDermott, he coauthored a book called "The Hunt for KSM: Inside the Pursuit and Takedown of the Real 9/11 Mastermind, Khalid Sheikh Mohammed." Josh, thanks so much.

MEYER: You're very welcome.

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