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Soon after Sept. 11, 2001, Attorney General John Ashcroft addressed the nation's mayors and police chiefs, announcing a paradigm shift in how the Department of Justice would handle terrorism cases:

"Let the terrorists among us be warned: If you overstay your visa -- even by one day -- we will arrest you. If you violate a local law, you will be put in jail and kept in custody as long as possible. We will use every available statute. We will seek every prosecutorial advantage. Our single objective is to prevent terrorist attacks by taking suspected terrorists off the street."

To carry out this objective, the FBI, the principal investigative arm of the U.S. Justice Department, began a metamorphosis into a threat-based, intelligence-driven organization -- in essence an agency like Britain's MI-5 -- while continuing to build cases and bring criminals to trial. Five years later, how is the transformation going?

"[We] have the task of not just investigating a crime after it has happened -- which is the old paradigm which we have done for decades -- we now have the duty to prevent that crime from ever happening in the first place," says McGregor Scott, the U.S. Attorney who prosecuted Umer and Hamid Hayat of Lodi, Califor. on terror-related charges.

For some at the FBI, prosecution is even beside the point in this new paradigm. "The mission is prevention," says Art Cummings, the special agent in charge of counterterrorism and intelligence at the FBI's Washington, D.C. field office. "And once I identify someone that I believe to be involved in terrorism, that person is but a means for me to collect against the possible operation."

This focus on preventing terrorist attacks has prompted concerns about civil liberties.

"More and more we've been shifting to ferreting out people who have bad thoughts and prosecuting that as a preventive measure, rather than arresting someone who has ... acted in a manner that violates the laws," says Michael Greco, former president of the American Bar Association. "And that's a slippery slope. Because how do you start to police bad thinking, bad thoughts? Where do you draw the line when you start down that path?"

It is a difficult line to draw in terms of resources as well. Thousands of man-hours are spent each day to, as Assistant Director of the FBI's Counterterrorism Division Larry Mefford puts it, "run every lead into the ground."

And this new mission is layered over the bureau's existing responsibility to investigate everything from violent crime to civil rights issues to corporate and health care fraud. To fulfill its expanded role, the FBI has been forced to realign resources and shift agents from some criminal programs to counterterrorism.

In May 2006, the Department of Justice Inspector General testified before Congress that during fiscal year 2004, the FBI had 2000 fewer field agents investigating traditional criminal manners than it had in fiscal year 2000 and had "opened 28,331 fewer criminal cases in FY 2004 than it had in FY 2000, a 45 percent reduction."

The Inspector General also found that the number of criminal cases the FBI referred to U.S. Attorney's offices declined by 27 percent over the same period.

Amy Zegart, a former National Security Council staffer and an expert on the intelligence community, wonders if, even with these changes, the FBI is up to the task.

"I think the FBI is exceptional at what it's always done for 80 years, which is catching criminals," Zegart tells FRONTLINE. "What the FBI is really good at is focusing on the past, solving the past crime, but preventing future events takes an entirely different set of skills, and the FBI just isn't an intelligence agency."

This article was a project of the Investigative Journalism for Print and Television Seminar at the University of California at Berkeley, Graduate School of Journalism, taught by Reva and David Logan Distinguished Professor Lowell Bergman and Rob Gunnison under the direction of investigative journalist Marlena Telvick. Reporting by Jeff Kearns, Charlotte Buchen, Jordan deBree, Cathy Bussewitz, Lee Wang and Center for Investigative Reporting intern Taylor Valore. Additional research by Matt Levin, Kate Golden and Joseph De Avila. Additional editing by Alison Pierce of the Center for Investigative Reporting. Special thanks to the Reva and David Logan Foundation and the Gruber Family Foundation.