Mueller does not typically sit for interviews. But recently he talked with Pelley at FBI headquarters.
Among the questions: Could the FBI have prevented Sept. 11, and with the first anniversary of the anthrax attacks next month, why the bureau hasn't made an arrest in that case. But most striking was Mueller's appraisal of al Qaeda and the danger it poses to the United States today.
"There is a committed group of al Qaeda operatives still out there that are committed to killing Americans, and to the extent that they can formulate and execute a plan in the United States, they will attempt to do so," he said.
Are there al Qaeda operatives in the United States today? "I believe there are people who are supportive of al Qaeda's goals, al Qaeda's missions. Yes, I think there are those individuals in the United States."
A plan developed fairly early on to disrupt the worldwide financing of al Qaeda. Has the U.S. disrupted their finances enough to prevent the kind of massive attack that we saw on Sept. 11?
"To the extent that we've been able to investigate what it cost to them, it was something in the range of anywhere from $400,000 to $500,000 at the max, which is not a substantial sum for an organization. And consequently, I cannot say that we have disrupted the organization to the extent that we have precluded them from finding the financing for an operation such as September 11th."
Mueller is a former federal prosecutor, who took over the FBI Sept. 4, 2001. The next week was Sept. 11. The next month brought the anthrax attacks. Since then there have been revelations that FBI headquarters missed crucial warnings before the September attacks. The latest came last week in Congress, when a New York undercover agent, testifying behind a screen, said headquarters wouldn't let him track down a suspect named Khalid al-Mihdhar.
The agent told the committee that he'd been working on the criminal investigation of the bombing of the USS Cole in Yemen. In August, 2001 the CIA told the FBI that al-Mihdhar was likely connected to the Cole bombing and that he was probably in the United States. The New York agent wanted to track him down but FBI headquarters said no, telling the agent that foreign intelligence information could not be used in a criminal investigation.
That's the way FBI lawyers read the law. The frustrated agent wrote headquarters, warning "someday someone will die… the public will not understand why we were not more effective…" Two weeks after that memo al-Mihdhar helped fly American Flight 77 into the Pentagon.
Judiciary committee chairman Patrick Leahy and Republican committee member Charles Grassley are among the senators with the most authority over the FBI.
"What this really shows is that there's a lot of very sincere, hard-working, very sophisticated agents at the local level that are doing the job the way it should be done. And people in headquarters are ignoring them," says Grassley.
Says Leahy: "Prior to September 11th, they had one analyst at the FBI working on al Qaeda matters, one, to give you some idea of the priority. They had, between the Department of Justice and the FBI, they had a whole task force working on finding a couple of houses of prostitution in New Orleans. They had one on al Qaeda."
Pelley's interview with Mueller came before the al-Mihdhar revelation. He asked about other leads that might have uncovered the Sept. 11 plot, including a July memo from a Phoenix agent who theorized that some Arab men in U.S. flight school might be terrorists.
If the FBI had done its best running down that theory, might Sept. 11 have been prevented? "I do not believe that we could have prevented September 11th," Mueller said. "There are thousand upon thousands of students going to flight schools in the United States, not only from countries around the world but particularly from middle eastern countries, and how would you differentiate these individuals who were the potential hijackers from the thousands of others from the middle east who were here in the united states legitimately obtaining training?"
But one did 'differentiate' himself. Zacarias Moussaoui had acted suspiciously at a flight school and was picked up three weeks before Sept. 11. But FBI headquarters ruled there wasn't enough evidence to search him. After the terror attacks, they found he had a German phone number linked to al Qaeda.
"That took us several months, to follow that lead, and it also required the full support of the German authorities, and it would have been very, I think impossible to have followed that particular lead in the days between the time in which Moussaoui was detained and September 11th," says Mueller.
The mishandled leads came before Mueller's watch. But looking back he's reached a conclusion: "I can tell you there are things I wish we had done differently. That there are things we should have followed up on. But the bottom line is I do not believe that we would have been able to prevent September 11th."
Might Sept. 11 have been stopped if they had paid more attention to the Phoenix memo, gotten the search warrant for Moussaoui and followed up on the New York agent's concerns? Says Leahy: "I have a sinking feeling that it could have been, but I don't know. I hope my feelings are wrong for the, for the sake of the country."
Senator Grassley worries that the people who ignored the warnings are still at headquarters. They should be fired, he says.
Mueller is making changes. He's put a terrorism task force in every U.S. FBI office. He's moved 500 agents into counter-terrorism.
Some of those agents are in Afghanistan. They're digging up burial mounds looking for Osama bin Laden and other terrorists. So far they haven't found anyone on the FBI's Most Wanted list.
Where is Osama bin Laden? Says Mueller: "If I knew, he would be hopefully not with us anymore. I think it's very difficult over in Afghanistan. If you've flown over some of that territory, you know how difficult it is. And it is not difficult for persons to hide, particularly if they can hide in supportive communities. And we just don't know."
Will we find him? "Sooner or later, yes," he says.
Another fugitive on his mind is the anthrax terrorist who killed five last year with letters to Congress and the media. Mueller says there's no arrest because there's so little evidence to go on: no finger prints, no hair, no fiber, no DNA.
The name of one former biological warfare scientist has come up in public, Mark Hatfill. But law enforcement sources tell us that he is not considered a more likely suspect than many others with similar backgrounds.
Mueller also believes that the anthrax terrorist will be caught.
But more than any one case, Mueller's biggest challenge is revolutionizing the FBI, an organization that critics say is still more in tune with Bonnie and Clyde than Osama bin Laden.
Given the FBI's new priority to prevent terrorism in the United States, what is the best guarantee you can make to the American people?
Says Mueller: "That every FBI agent understands that the mission of the FBI is to take any piece of information that comes to our attention, and put it into a framework where we can look at it and determine whether or not there is something there to prevent another terrorist attack. Nobody in the bureau wishes another September 11th."