At the small mosque in the gritty southeast section of Lodi, Calif., many Pakistani men arrive to worship wearing the traditional shalwar qameez, a long shirt and loose-fitting pants. More than a year after federal authorities, with the help of a Pakistani-American informant, tried a father and son on terrorism-related charges and deported two imams, these worshippers, and much of the rest of Lodi's large Pakistani community are skeptical of outsiders, reluctant to talk for fear of inviting scrutiny or surveillance by federal authorities.

"We were making tremendous progress in this community, but we've been significantly set back," Taj Khan, a leader in Lodi's Muslim community who has worked to strengthen ties between Pakistanis and local police, told FRONTLINE. "You can't exaggerate the damage done by the FBI's investigation here."

At the time of the arrests in 2005, several members of the community say they were questioned, intimidated and even followed by FBI agents. More than a year later, few in the community are willing to talk to the media because the FBI has said it has not ended its investigation. Some even suspected that reporters covering the trial were government agents.

The alienation that followed the Lodi investigation is part of a broader national trend in which Muslim Americans feel they are first considered suspects, not partners, in anti-terrorism efforts. Since 9/11, the government has unnerved Muslim Americans by conducting surveillance on mosques, eavesdropping on phone calls and emails and even questioning people with little apparent cause.

In December 2005, U.S. News & World Report revealed that beginning after the 9/11 attacks and lasting through 2003, the federal government had monitored radiation levels at Muslim businesses, homes and mosques. In a meeting with Muslim- and Arab-American leaders in January of 2006, the FBI explained that the classified program was based on intelligence that terrorist cells had infiltrated the United States, trained to blend into Muslim communities and to possibly use a dirty bomb. No such cells, however, have been found.

And in 2002, hundreds of Arab and Muslim men were fingerprinted, photographed and questioned as part of a Immigration and Naturalization Service's (INS) program called Special Call-In Registration. "This INS roundup is confused, ineffective and deceptive," said Salam Al-Marayati, Executive Director of the Muslim Public Affairs Council. "It is clear these measures erode our freedom, yield no enhanced security and serve to damage America's global image."

Top government officials seem aware of the need to engage the Muslim community. "We must not only work across federal, state and local government to prevent domestic terrorism," Homeland Security Secretary Michael Chertoff said in 2006, "but we must build a new level of confidence and trust among the American Muslim community, who are critical partners in protecting our country."

Chertoff's statement was underscored by two recent widely publicized terrorist plot disruptions. In June 2006, a Canadian-Muslim informant aided authorities in arresting 17 people allegedly plotting to launch a series of Al Qaeda-inspired attacks using fertilizer bombs and to behead the prime minister. And in August 2006, British officials, following a tip from a Muslim informant, arrested 24 people accused of planning to blow up 10 U.S.-bound jetliners.

President Bush called the arrests "a stark reminder that this nation is at war with Islamic fascists." But the phrase "Islamic fascists" sparked controversy and criticism from the same community his administration hoped to court. "We believe that this is an ill-advised term, and we believe that it is counterproductive to associate Muslims with fascism," said Nihad Awad, Executive Director of the Council on American-Islamic Relations

At the same time, several polls since 9/11 indicate many Americans have skeptical attitudes about Muslims. In 2004, 44 percent of respondents to a Cornell University survey agreed that "some curtailment of civil liberties is necessary for Muslim Americans." And in 2006, a Washington Post-ABC News poll showed nearly half of Americans held some negative views of Islam.

Some law enforcement experts maintain it is vital that they build relationships with the tight-knit Muslim community. "If they work closely with the community, they'll find that fundamentalist sooner than any informant would, no matter how much money they pay," said Jim Wedick, a former FBI agent who served as an unpaid consultant for the defense in the Hayat case. "They know more than anybody else if somebody comes in and starts to preach fundamentalist ideas."

To that end the FBI threw its support behind the Partnering for Prevention and Community Safety Initiative, a program run by Northeastern University which sought to improve counterterrorism efforts while protecting Arab, Muslim and Sikh communities from discrimination and preserving civil liberties.

The initiative aimed to share the best practices of FBI field offices most familiar with Muslim communities with all 56 field offices. "Fifty-six offices work bank robberies in one way, not 56 ways," said Michael Rolince, a 31-year FBI veteran who was special agent in charge of counterterrorism in the Washington field office from 2002 until his retirement in 2005.

"After 9/11, I was of the opinion that we didn't have the kind of inroads into the community that we needed to have," said Rolince, now a counterterrorism consultant at Booz Allen Hamilton. "We didn't know what was in our own backyard, so I started with the approach that we're not here to intimidate you, we're here to help."

Despite the initiative's promise and its backing within the community and the FBI, the agency rescinded its initial $1 million pledge to the program. Rolince said that FBI higher-ups decided to shift much of the budget to pay for Sentinel, the latest version of the troubled case management database whose price tag is running into the hundreds of millions. In addition, he said there was opposition from a few bureau hardliners who saw outreach as "working with the terrorists."

"The FBI stepped down, and it doesn't leave them in a good place," says Deborah Ramirez, Northeastern law professor and founder and executive director of the initiative, who spent two years briefing the FBI on its progress. Ramirez said the bureau has taken an ad hoc approach to reaching out to Muslims. "The Muslim community are our best allies; they know the language, the culture the history. Without them we are flying blind."

"We need bridges to this community," she told FRONTLINE. "We have handmade bridges when we need superhighways."

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.