During his confirmation proceedings, Mueller said it would be a "high privilege" to lead the bureau. In what colleagues say is his typical straight-forward manner, he also made clear that he planned broad changes, particularly in the FBI's management structure.
"I think it's a wonderful institution," Mueller said. "I think it has problems."
No time for changes
But as he helps lead the sweeping investigation of the Sept. 11 attack, Mueller must work with the bureau as it was when he arrived, whatever its shortcomings.
Instead of sticking to his mandate for reform and increased accountability, Mueller is part of the administration team asking Congress to grant new powers to federal law enforcement such as broader authority to conduct eavesdropping. Instead of cleaning house, he's going with what he's got to help guide the massive manhunt and detect any new threats.
When Eric H. Holder Jr. was deputy attorney general under former President Bill Clinton, he recommended in 1998 that the Republican Mueller be tapped to help turn around the federal prosecutor's office in San Francisco. Holder said Mueller's team knows what it is doing, in spite of the FBI's recent troubles.
The bureau is doing what it does best, Holder said, undertaking a major investigation and using all of its expertise.
"There's a cadre of really good people at the bureau, despite the fact that the bureau has had a number of problems recently," Holder said.
Some 7,000 agents and support staff are working on the case, codename PENTTBOMB, with Deputy Director Thomas J. Pickard serving as the case agent. Since the first hours after the terrorist strikes, the bureau's Strategic Information Operations Center has been in crisis mode, working in a fifth-floor conference room inside the J. Edgar Hoover Building on Pennsylvania Avenue.
A sterling reputation
Unlike his predecessor, Louis J. Freeh, Mueller never was an agent before he became director. But with a long history as a federal prosecutor, he hardly is an outsider. Mueller started his law career in the San Francisco U.S. attorney's office. During the administration of George Bush, he rose to head the Justice Department's criminal division.
Friends describe Mueller as a no-nonsense iron man. When he returned to the federal prosecutor's office in San Francisco in 1998, he began his overhaul by sending this clear-cut directive to every lawyer in the office: Justify your job. He started work at the FBI just weeks after undergoing prostate surgery.
Mueller was born into an affluent family in New York, attended St. Paul School, an exclusive prep school in Concord, N.H., and graduated from Princeton University. He then joined the Marines. He served as a rifle platoon commander during the Vietnam War, earning a Bronze Star, a Purple Heart and the Vietnamese Cross of Gallantry.
In the mid-1990s, Mueller was earning $400,000 a year as a senior partner at the Boston law firm Hale & Dorr when he called up Holder in the Justice Department and said he wanted to return to the courtroom.
Holder gave him a job as a line attorney, prosecuting homicides in the District of Columbia. It was considered an astonishing career move at the time. Now, Holder said, it should serve Mueller well as he works on the terrorist attack case.
"A lot of what you do as a homicide prosecutor is to figure out, `Who did it?'" Holder said.
In the month since the attacks, FBI agents have chased some 300,000 leads to do just that, following a trail from flight schools in Florida and Phoenix, Ariz., to apartment complexes in the Maryland suburbs.
While the FBI has assembled quick sketches of the 19 suicide hijackers, no charges directly related to the attacks have been filed. And the detention of nearly 700 people, many of them of Middle Eastern descent, has raised concerns among immigration advocates and from Muslim leaders, who say the bureau is unfairly targeting their community.
New York lawyer Stanley L. Cohen represents an Islamic cleric living in Laurel who refused to meet with FBI agents after the attacks. The cleric, Mohammed al Hallak, later talked to federal prosecutors, but he complained about his treatment by the FBI.
"A month ago, the entire country was saying, `What's wrong with the FBI? They're screwing up cases left and right,' " Cohen said. "You want to know why the same institution now singled out my client? The answer lies in the recent past."
In Congress and in official Washington, the sharp criticisms of the bureau that were so prevalent in recent years now are mostly muted. But that is not likely to last. Already, some have questioned why the FBI failed to apprehend two suspected Pentagon-crash hijackers - Khalid Almihdhar and Nawaf Alhazmi - whose names had been on a government watch list since Aug. 21.
Other concerns also persist. In a letter to Mueller just two weeks after the attacks, Sen. Charles E. Grassley of Iowa raised a caution about lapses during the Waco, Trans World Airlines Flight 800 crash and Oklahoma City bombing probes.
"I know we both want to ensure the FBI is not hobbled by an ineffective system for managing key investigative information," said Republican Grassley, a sharp critic of the bureau.
Mueller has denied that the bureau is targeting the Middle Eastern community. He has not commented more broadly about how the bureau's problems in the recent past could hamper the current investigation. But in a visit to New York 10 days after the attacks, Mueller promised that in this case, the bureau would deliver.
"When you think of 6,000 souls who were lost here, it is very difficult to grasp the enormity of the loss and the unspeakable horror perpetrated by mass murderers," Mueller said as he inspected the rubble at the site of the World Trade Center towers. "And we in the FBI, law enforcement, here and in other cities around the country, will not sleep until they are brought to justice."