In July 2005, police in Torrance, Calif., arrested two suspects in a string of gas station robberies. But what seemed a run-of-the-mill felony case turned exceptional when police found documents detailing a terrorist plot in the suspects' apartment. In an indictment the following month, prosecutors alleged the men were using proceeds from the robberies to bankroll planned attacks on targets in the Los Angeles area, including military installations.

In part because of threats like this, the Department of Defense (DoD) now has expanded its role in homeland defense and domestic intelligence. The transformation began a few weeks after 9/11, when the DoD released its Quadrennial Review announcing its new priority: homeland defense.

"The challenges the Nation faces do not loom in the distant future, but are here now," wrote military planners in the document. "They involve protecting our critical bases of operation -- including the most critical base of operation, the U.S. homeland."

Among new initiatives aimed at fulfilling this mission are NORTHCOM, a new military command responsible for defending the United States; JRIES, an online system to share information with local law enforcement; and CIFA, a new intelligence agency focused on culling information on threats at home.

NORTHCOM -- Homeland Command

In October 2002, one year after announcing its new mission, the Pentagon took the unprecedented step of creating a domestic military command, NORTHCOM. Based in Colorado Springs, Colo., NORTHCOM's mission is to "deter, prevent, and defeat threats and aggression aimed at the United States."

"NORTHCOM is a fundamental recognition that terrorists consider the United States homeland to be the preeminent battle space in a global conflict," said Assistant Secretary of Defense for Homeland Defense Paul McHale. He emphasized that the bulk of the new mission focuses on the military's response in the event of an attack on the United States. For example, in a chemical weapons attack NORTHCOM could deploy specialized teams to minimize the damage, aid with clean-up and maintain public order.

But crisis-response teams aren't the DoD's only asset. It is a huge player in the intelligence community, controlling approximately 80 percent of the nation's intelligence budget. After 9/11, some of these intelligence resources began to hunt for terrorists possibly hiding inside the United States.

At NORTHCOM, this new task was taken up by a staff of 90 intelligence analysts, but NORTHCOM was only the tip of the iceberg. In the months after 9/11, several DoD programs pushed into domestic intelligence in a way not seen in three decades.

JRIES -- Sharing with Local Police

It was back in the 1970s that congressional hearings exposed surveillance by the military and other intelligence agencies on thousands of political activists in the United States. Pat Duecy, a former Navy officer, joined the Pentagon's Defense Intelligence Agency in the midst of those hearings. Duecy recalled the mood inside the DoD. "It was a difficult time," he told FRONTLINE. "There were a lot of concerns about oversight, because the intelligence community seemed to continue to do stupid things at home."

In response, the Pentagon put in place new restrictions on domestic intelligence: The Pentagon could only collect information on persons residing in the United States if they were working on behalf of a foreign power, plotting to attack military assets or actively engaged in criminal activity targeting the Department of Defense. Any information collected on U.S. persons outside those guidelines was to be redacted or purged from military databases.

These regulations led to a bureaucratic culture averse to any activity with a domestic tinge. "We had been told in years past, 'Don't even think, don't even dream about doing domestic stuff,'" said Duecy, recalling a conversation with a superior, "'because you'll all go to jail and you'll take me with you.'"

In August 2001, Pentagon officials asked Duecy to assume control of the DoD's Joint Intelligence Task Force on Counterterrorism (JITF-CT). Barely a year old, the task force was charged with identifying potential terrorist threats. During that first month, Duecy paid little attention to what might be happening inside the United States; that, after all, was largely off-limits. Instead, his team of approximately 50 analysts focused on culling data from abroad.

Everything changed on 9/11. U.S. officials were desperate for information, but DoD's regulations on domestic intelligence meant Duecy's task force had little to go on. Analysts turned to the FBI for help. "We couldn't get anything out of the FBI because they didn't really know what the threat was either," said Duecy.

Duecy and his colleagues scrounged for leads. It was in the midst of this search that the task force found itself sharing information with local police departments around the country. What would eventually evolve into a nationwide program started with a fax machine.

The first faxes came from police officers in New York and Los Angeles who were friends with military reservists assigned to the JITF-CT. Unable to get useful information elsewhere, police were sending their leads to Duecy's analysts. The inquiries ran the gamut from potential surveillance of military installations to routine traffic stops that had left an officer suspicious. Duecy's team checked those leads against federal intelligence databases and relayed back the results.

As the number of faxes grew, Duecy and his team had to determine whether this exchange with local police was even legal. "We figured, gosh, we better make sure we can do this," Duecy said. Reading the regulations, he was pleasantly surprised. "The actual laws allow for quite a lot if you can establish reasonable justification for suspicion."

Reassured, Duecy transformed the fax-based system into an encrypted Web site called the Joint Regional Information Exchange System (JRIES). Deputy Chief Mark Leap, director of counterterrorism for the Los Angeles Police Department, told FRONTLINE that in 2001 and 2002 JRIES was the LAPD's primary link not only to the Department of Defense, but also to other police agencies. "What that allowed us to do is enter, for lack of a better description, a chat room where we could post information and get information from other law enforcement agencies," Leap said. "And it worked very well."

CIFA -- Data Mining Gone Too Far?

As JRIES ramped up, there was a parallel build-up in another corner of the Pentagon. In February 2002, then-Deputy Secretary of Defense Paul Wolfowitz authorized the creation of the Counter-Intelligence Field Activity (CIFA). According to David Brandt, former head of the Naval Criminal Investigative Service (NCIS), the aim of CIFA was "to ensure that our operational activities -- Army, Air Force, Navy, Marine Corps -- are consistent with what each other, strategically, should be doing."

Each service branch maintains their own databases, logging suspicious activity around and inside military installations. CIFA consolidated that information and checked it against other intelligence and law enforcement databases.

CIFA has also been credited with much of the DoD's post-9/11 data mining, a technique that searches vast troves of information for suspicious patterns. Cynthia Wynkoop worked for several years as the special assistant to CIFA's director, and like the majority of CIFA's staff, she was a private contractor. Wynkoop told FRONTLINE that CIFA analysts were trolling both intelligence databases and public domain sources looking for patterns.

"The term 'data mining' has really been used negatively by the press to associate it with government spying," she said. "We have this information that's available, that's public. Why would the Department of Defense, as well as other agencies, not use it?"

Others are less sanguine about CIFA's activities. "Over the years, we've been very careful in the way we've handled the collection of information where we knew that U.S. citizens were going to be involved," said Elizabeth Rindskopf Parker, former general counsel for the National Security Agency and the Central Intelligence Agency and now Dean and Professor of Law at McGeorge School of Law at the University of the Pacific.

"This requires a great deal of care and training, rules and regulations, and if we're really now planning on turning any part of that over to the military, we're going to see they're not going to have had adequate training. There are going to be mistakes, and people are going to be very unhappy."

In fact, CIFA's intelligence activities drew fire in December 2005, when NBC News reported that the agency had been conducting surveillance on more than 20 activist groups around the country, including a Quaker anti-war group called The Truth Project and several student groups protesting the military's "Don't Ask Don't Tell" policy towards gays in the military.

The surveillance was part of a "neighborhood watch" program called Threat and Local Observation Notice (TALON), which collected reports of suspicious activity around military bases from service members, their families, local law enforcement and even ordinary citizens.

Rindskopf Parker isn't surprised. "Once you start gathering intelligence in a domestic setting, you take one step and the next step follows," she said. "Now it's moving beyond simply a defensive line and [becoming] more offensive."

The leaked TALON reports led to a congressional probe in 2006. In response, the Defense Department says it has ordered that TALON records on demonstrators be removed from the database.

"It's déjà vu all over again," said Christopher Pyle, former Army intelligence official famous for blowing the whistle on the Army's domestic spy program in the 1960s. "In those days, they were concerned about communism; these days we're concerned about terrorism. The vacuum cleaner works the same way."

Adapting to the New Mission

While CIFA has drawn criticism for aggressive tactics, JRIES fell victim to what Pat Duecy saw as an overabundance of caution. In the fall of 2003, as the Pentagon faced mounting criticism over a proposed data mining program called Total Information Awareness, Vice Admiral Lowell Jacoby, director of the Defense Intelligence Agency, ordered Duecy to shut JRIES down.

"My boss got very, very worried about the program," Duecy recalled. "He said, 'I don't want it in my shop. Kill it.'"

Duecy told FRONTLINE he doesn't believe JRIES ever crossed a legal boundary, but with no alternative he transferred the program to the Department of Homeland Security (DHS), where it has suffered setbacks. Three years later, DHS's Inspector General issued a report (pdf file) criticizing the program's near-total collapse.

CIFA and JRIES's troubles are indicative of opposite forces at play -- overreaching versus caution -- as the military adapts to its new role in defending the homeland. Christopher Pyle hopes the history of the 1960s and 1970s regarding the military's domestic intelligence activities will be instructive. "I hope that we're re-educating ourselves," he said. "Every generation has to learn the basic principles over."

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.