BOSTON — On a cold, gloomy day in February of last year, a group of protesters showed up at the U.S. attorney’s office here and demanded to see a prosecutor who had brought a terrorism case against a young Muslim man.

They had spent the week pursuing Aloke Chakravarty, an assistant U.S. attorney, bombarding him with faxes and phone calls and accusing him of what may be the most serious affront to a government lawyer: targeting Muslims because of their faith.

But it was not just any prosecutor who had aroused the ire of some in Boston’s Muslim community. Chakravarty had shaped his career in part around protecting the civil rights of that very group, feeling it had been unfairly targeted by bigotry. And he had been leading the Justice Department’s efforts to create a new relationship with Muslims throughout the region.

He also was the man who had prosecuted several Muslims in terrorism investigations. Now, he found himself under attack.

A decade after the Sept. 11, 2001, terrorist attacks, the dilemma for Chakravarty and other federal officials — searching for homegrown terrorists without violating the rights of Muslims — remains as sharp as it was in the immediate, chaotic aftermath of the attacks.

The federal government’s domestic counterterrorism efforts have scaled up dramatically, largely through a transformation of the FBI into an intelligence-driven agency and a large increase in the number of agents devoted to fighting terrorism. Justice Department and FBI officials say they have helped prevent a second major attack on American soil and arrested numerous would-be terrorists.

The government’s efforts have relied in part on a more trusting relationship with Muslims — a particular focus in the Obama administration — and many leaders in the community have been open to that. But others have complained about federal law enforcement and its investigations, surveillance and arrests of Muslims, accusing officials of targeting the same community they are trying to cultivate.

It is one of those arrests and prosecutions that has complicated Chakravarty’s dual role: From his office next to Boston Harbor, he has taken the lead in trying to build a better rapport with Muslims. But he also is prosecuting the terror case against Tarek Mehanna, a local Muslim whose trial is scheduled for early October.

In meetings with Muslims, Chakravarty is unfailingly polite and solicitous. In court, he is the tough post-Sept. 11 prosecutor, endorsing tactics that are considered routine by law enforcement officials but have infuriated many Muslims, including the use of cooperating witnesses in their community.

Arguing in court that Mehanna should be held without bail, Chakravarty described the thread between the accused and those around him.

Mehanna committed his crimes “often from the confines of his own home,” Chakravarty said, “often with the assistance, with the knowledge of people in this very same community.”

In the Boston area, tensions between federal law enforcement and Muslims, who number roughly 100,000, were triggered by the 2001 attacks, when 10 hijackers boarded two planes at the city’s Logan International Airport and crashed them into the World Trade Center.

That prompted a crackdown by the FBI’s Boston office, whose jurisdiction stretches from Rhode Island to Maine. Agents fanned out, rounding up local Muslims for questioning, according to Boston area Muslims. It was part of a nationwide sweep that ultimately brought in hundreds of people, most of whom never faced terrorism-related charges.

“There was huge investigative activity after September 11,” said Richard DesLauriers, special agent in charge of the FBI’s Boston office.

Aloke Chakravarty watched the crackdown with unease from the Massachusetts attorney general’s office, where he was an assistant attorney general, and decided to do something. He pursued a job at the Justice Department, convinced that he could help strike “that balance between civil liberties and how invasive law enforcement can be,” he said.

“It became clear that people from certain backgrounds, largely Arab, Muslim, South Asian backgrounds, had shortly after the attacks been treated differently, both in the public eye as well as literally in terms of the enforcement of our laws,” he said in an interview.

When Chakravarty arrived in Boston in 2005, law enforcement officials had already come to appreciate the need to reach out to Muslims. Justice and FBI officials had been speaking at mosques and organizing meetings with Muslim leaders, trying to form bonds and smooth over the resentment that had built up.

The hope was that if Muslims trusted federal agents, they would be willing to alert the government to possible threats. And, especially after the terrorist attacks, the effort was aimed at protecting Muslims amid a spike in prejudice against them.

It was a personal mission for Chakravarty, 38, a graduate of Baltimore’s Johns Hopkins University who speaks with a scholarly air and has a trim goatee flecked with gray. Known as “Al,” he is uncomfortable discussing personal details and would not disclose his religion. He did say he was born in South Carolina, where, he notes with pride, the governor, Nikki Haley, is Indian-American.

It was presumably his Indian heritage that, years earlier, prompted a defendant to blurt out across a courtroom the word “terrorist” when he saw Chakravarty, who at the time was a prosecutor in Middlesex County near Boston.

When he joined the U.S. attorney’s office, law enforcement’s attempt to work with Muslims was troubled. The FBI was about to rescind funding to help start a Boston-based program to coordinate efforts to reach out to Muslims and Arab Americans nationwide.

The agency cited budget problems, but Deborah Ramirez, a Northeastern University professor who designed the program, said officials also “got a lot of political push-back and decided they couldn’t move forward. . . . There were some who said you shouldn’t be sitting down with these people, you should be treating them as suspects.”

It was unclear whether the meetings in Boston would continue until Chakravarty, working with Muslim leaders, pushed to keep things going. It was, he recalled, a “watershed moment where there was no funding, no infrastructure, no governmental doctrine or mandate” for what he saw as a critical effort.

Since then, the efforts have expanded. Chakravarty’s boss, U.S. Attorney Carmen Ortiz, is focused on building a relationship particularly with the largely Muslim Somali community. The head of the FBI office, DesLauriers, convenes his own meetings with Muslims and other minorities.

And the monthly meetings that Chakravarty had spearheaded and often runs, known as “Bridges,” have become established, routinely drawing high-ranking officials, including Ortiz, representatives of the FBI and numerous Muslim leaders. The conversation can range from airport security to visits from FBI agents, and, in a recent session, how to combat anti-Islamic stereotypes.

A regular participant is Abdillahi Abdirahman, a coffee shop owner who represents the city’s roughly 4,000 Somali Muslims.

Abdirahman, who also meets on his own with the FBI, says he often complains during the meetings about visits from agents to Somali homes and businesses. FBI agents have come to his coffee shop at least 15 times in the past two years, he said. They ask if he knows anyone affiliated with al-Shabab, a Somali Islamist extremist group that is linked to al-Qaida. They are polite and professional, he said, and always take notes.

Still, he added, “they are harassing the community.”

His meetings with FBI supervisors are cordial, he said. They listen to his concerns and offer to help. They too quiz him, scribbling in their notebooks. But despite the kind reception from supervisors, he said, the agents keep coming back.

“The people at the top say ‘we’re partners, we care,’ ” said Abdirahman. “But the message from management and the message from the soldiers on the field doesn’t totally connect.”

And, he said, some people in his own community are suspicious of him because of the meetings.

Ziad Ramadan, another Muslim leader, said he meets with FBI counterterrorism agents a few times each year at the Worcester Islamic Center, about 40 miles from Boston, where he sits on the board. They sit in his second-floor office, ask how they can help the mosque, then question him about his congregation.

“They ask, ‘Do you know this guy, does he go to the mosque?’ ” Ramadan said.

He believes agents are profiling Muslims but says he is grateful for their assistance. “We’re on the same team, ” he said. “The most likely terrorism case will come from the Muslim community.”

Yet Ramadan cannot reconcile his warm relationship with the FBI with the terror case the agency built against Mehanna. Mehanna belonged to Ramadan’s Worcester mosque and taught at the adjoining Islamic school. His arrest and treatment has outraged Ramadan.

“This guy is not a threat, I would bet my life on it,” Ramadan said just after the close of a recent midday Thursday prayer. “They have to lock him up 23 hours a day? There’s no justification for that.”

“I’m completely perplexed,” he added.

At the federal offices in Boston, Chakravarty and FBI officials are balancing many strands in their complex relationship with Muslims.

Cynthia Deitle, who runs civil rights enforcement efforts for the FBI office here, finds herself walking a fine line. While she is seeking out victims of civil rights abuses, she said, she sometimes fields complaints from Muslims about visits by counterterrorism agents. She tries to assuage the concerns but also feeds tips gained from those sessions to her colleagues on the terrorism side.

“How do we balance these two programs?” she said. “Every time the relationship is challenged, every time the trust is cracked, we have to find a way to repair it, because it’s going to happen over and over. It’s a continual challenge, both on the terrorism side and on my side, to keep encouraging people, especially in that community, to talk to us. And to trust us.”

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