“This comes as a shock,’’ Regan said. “All of our workers are treated with respect.’’

“They took advantage of me, but not only me — everyone,’’ Chico said through a translator. “I felt humiliated that I work and work and I was not valued.’’

“We were the ones who made Upper Crust as big and as rich as they are, but I suffered very much,’’ said Washington “Chico’’ Rodrigues da Silva, who followed his brother Marcos from Marilac to Boston in 2003. With the money they earned at the second Upper Crust store, in Brookline, the siblings paid $35,000 to buy their family in Marilac a small avocado-colored house. But plans to start their own business were abandoned after Marcos was deported. Since returning to Marilac last fall, Chico has spent his days milking cows and herding cattle, and lacks a steady income.

Meanwhile, in dusty Marilac, some fear a reliable source of income used to build farms and businesses and houses will vanish. Others say the village will be better off without the pizza money and the sacrifices it requires.

Over time, however, this amicable but unlawful relationship would unravel. Documents from a recent class action lawsuit show that as Tobins expanded his pizza empire, he began to exploit his immigrant workers. The employees took their complaints to the US Department of Labor, which ordered the chain to dole out hundreds of thousands of dollars in back pay. The department is now investigating wage violations at Upper Crust for a second time.

Tobins needed lots of kitchen help; the Brazilians worked hard and didn’t complain about workweeks that routinely stretched to 80 hours. Marilac prospered as Upper Crust’s immigrant employees sent thousands of dollars home, and the company swiftly expanded from its original store in Beacon Hill to one upscale suburb after another.

Over the past decade, dozens of men from Marilac have made the 7,500-mile trek, risking arrest, deportation, and, in rare cases, death. And Upper Crust, founded by Sharon native Jordan Tobins in 2001, welcomed them.

The most coveted destination has long been Boston — more precisely, one high-end local pizza chain. The promise of a job at an Upper Crust shop, passed by word of mouth from one villager to the next, offered the possibility of wages unheard of in Marilac, a community of 4,140 people in the mountains of southeastern Brazil.

MARILAC, Brazil — In this remote valley of sugarcane fields and cattle farms, where horses and bicycles outnumber cars and poverty binds the community like mortar, people searching for a better life have one choice: They can leave town.

As the business grew, more men in Marilac left behind girl-friends, fiancées, wives, and children to come to Boston, according to interviews with about 30 former workers and relatives of current and former workers. They easily found smugglers — called coyotes — to arrange their trip from Brazil: the bus to Sao Paulo, a short stay in Mexico City, and, finally, the border crossing — sometimes in an inner tube across the Rio Grande. Over time, at least 80 men from Marilac set up a colony of sorts in East Boston. Many lived together in crowded apartments near Maverick Square. Botelho, the inspiration for the “Lucky Luciano’’ Brazilian pizza on Upper Crust’s menu, frequently put up new arrivals at his home and gave them food and clothing.

“[Botelho] has always been competent and dedicated,’’ Regan said. “He was never asked to locate employees from a particular area, but it is hardly surprising that he would know more people from the area where he came from. Any person recommended for employment by him would have to be considered seriously.’’

Marilac provided a pipeline of cheap, dedicated workers for Upper Crust. In 2002, Luciano Botelho arrived with a decent command of English and an easy smile. Tobins tapped the Marilac native to oversee the hiring of the cooks and delivery workers who would become the backbone of the operation. Botelho, who is still employed by Upper Crust, declined to comment for this story.

It typically took a year of grueling six- and seven-day workweeks for the illegal immigrants to pay off the $10,000 to the smugglers who arranged their journey. After the obligation was settled, the men would send hundreds of dollars each month to family back in Marilac. Jose da Silva built a bakery and a house in just a few years, Jose Bento saved his troubled butcher shop on Rua Rio De Janeiro, and Pedro Chaves de Souza bought land and some cows on the outskirts of town.

Word of employment opportunities at Upper Crust spread. Others from Marilac began arriving. It felt like a family for the Brazilians in the shop. Tobins and other managers worked side by side with them, spinning dough and delivering pizzas on bicycles.

Pedro Chaves de Souza was among the first to come. He slipped over the Mexican border in March 2001 and came to Boston looking for work. A cousin introduced him to Tobins, who had just opened a pizza shop on Charles Street, in Boston’s Beacon Hill neighborhood. De Souza landed a job preparing vegetables in the kitchen. He earned about $8 an hour — well over the minimum wage at the time — and far more than he made working at a butcher shop in Marilac.

IN THE BEGINNING, the arrangement between Marilac and Upper Crust seemed just right, at least to those willing to risk the illegal passage and furtive toil.

Valdeir Pereira Pinto, 27, was a member of the group that lived in Hingham. In 2006, he left his Marilac home — a pink concrete structure with gaping holes like missing teeth where there should have been windows — and came to the South Shore town, one of the wealthiest suburbs in Massachusetts. He quickly found his new living arrangements were not much of an improvement over what he left behind.

For its Hingham restaurant, the fifth to open, Upper Crust set up an apartment for the immigrants near the shop, according to Joyce, who collected rent in cash from workers, then paid the building’s landlord with a check from the store’s account.

“The stakes got higher, and it got more cutthroat,’’ said Joyce, who said he left in June after becoming frustrated by the working conditions. “It was unbearable.’’

At the same time, some of the Americans who staffed the chain’s counters and worked as managers received raises, they say. Tobins prospered more visibly, using his newfound wealth to pay for expensive cars, a fancy boat, and even a private plane.

UPPER CRUST began to cut corners on labor costs as it grappled with expansion, said Patrick Joyce, a former operations manager who worked at Upper Crust for seven years. The immigrants say they took on more hours. The bonuses and employee parties that had sweetened the job ended, and requests for raises were regularly rejected. The Brazilian currency — called the real — was also getting stronger, so the workers’ dollars didn’t go as far back home.

Da Silva said that he began working at Upper Crust just a few days after arriving in Boston in 2003, and that within four years he had made enough money to buy apartments to rent out in Sao Paulo and to build an expansive house in Marilac with porcelain tile floors, crown molding, and the only green lawn in town. To this point, the Upper Crust story was not an unusual one at a time when many small businesses in America, especially in the restaurant industry, rely on illegal labor. The risks of exposure are small: There are roughly 11 million illegal immigrants in the country, including about 160,000 in Massachusetts, and it is impossible for authorities to check every workplace.

“I wanted to have a better future than I had if I stayed in Brazil,’’ said Dimas da Silva, who said he crossed through Mexico under the floorboards of a pickup truck, hiding among cans of gasoline to mask his scent from the trained dogs used by US border guards. “In USA, you can work hard and stay there for a few years saving money, and you can come back to Brazil and have a nice life.’’

They thought they had found a way out a few months later, when a Brazilian man stopped by the Brookline restaurant and handed da Silva the phone number of someone who he said could sell them an authentic green card, permanent resident identification that authorizes a foreigner to live and work in the United States. But it was part of an immigration sting. Da Silva was arrested in August 2007, along with Botelho and other illegal Upper Crust workers who had tried to buy immigration documents. Da Silva spent eight months in prison before being deported in 2008.

“I just dream about leaving Upper Crust and getting a better place to work,’’ Marcos Rodrigues da Silva said.

So they devised a plan. Da Silva and his relatives, including his uncle Edmar da Silva, began putting away of thousands of dollars that they hoped one day would finance their own pizza shop in Massachusetts.

A few hours later, Botelho called da Silva. He and Filho still had jobs if they wanted them, Botelho said. The men said they returned to work because they had bills to pay in Boston and families in Marilac who needed money. Besides, they believed their illegal status made them beholden to an employer who they said had repeatedly threatened to call immigration officials.

“Marcos and I cried because [Tobins] said we were selfish,’’ recalled Filho, speaking in his native Portuguese. His father, a Marilac native, followed him to Upper Crust.

Da Silva, who entered the country with a fake passport he bought in Portugal, told Tobins that employees were planning to strike unless they received raises or overtime pay. Tobins became incensed. They didn’t have any rights, he shouted, according to three former workers and a manager present at the meeting. If they wanted more money, Tobins said, they should find another job. Then he fired da Silva and Filho on the spot.

Filho and da Silva decided to meet with a lawyer to figure out their options. Then da Silva asked Botelho — the go-to guy to get Tobins’s attention — to arrange a meeting in the winter of 2006 at the Brookline restaurant in Coolidge Corner.

Sergio Soares Lima Filho Jr. and Marcos Rodrigues da Silva were more than tired. They were upset after finding out illegal workers at some other area restaurants were receiving time and a half after 40 hours. Upper Crust’s practice was to write one check for a worker’s first 40 hours, and an additional check, at the same rate, to cover extra hours. Some workers said they were paid entirely in cash.

“I just worked all the time, 80 hours and sometimes more,’’ Pinto said. “They said they were too busy, and, ‘I can’t give you [time] off; you must work.’ I was very tired.’’

Pinto was one of six workers crammed into a two-bedroom apartment. They paid about $1,200 total in monthly rent to Upper Crust, but spent most waking hours at the small pizza shop — a five-minute walk away. They rarely saw their Marilac friends in Boston.

Da Silva and Filho “were never threatened or fired, and they continued to work for the company until they were arrested,’’ Regan said.

After the arrests, Joyce, the operations manager, said Tobins told him to meet with a lawyer who could help get Botelho out of jail. While the other workers accused of being in the United States illegally fled or have since been deported, Botelho received a voluntary order of departure, according to the Department of Homeland Security, which means he has a designated amount of time to leave the United States. He is currently appealing to stay in the country longer.

Regan said the deportations had nothing to do with the restaurants.

“This case did not involve the company,’’ he said. “A couple of the company’s employees were charged as part of this sting and deported. [Botelho] was not charged and thus was not deported.’’

. . .

BY 2009, despite a deepening recession, Upper Crust was on a tear. It had 14 stores, a plan to open three more, and projected annual sales of up to $16 million, Tobins said in an interview with the Globe at the time. But the chain’s team of workers did not expand as quickly. To make up for the shortage of help, cooks were often rotated between stores and worked up to 100 hours a week to fill the gaps, according to Greg Goncharov, a former business manager at two of the chain’s restaurants.

The stores were adequately staffed, Regan said.

“I was so exhausted; I thought I wouldn’t make it there and come back,’’ Luis Lucas da Silva said through a translator. The Marilac native returned to Brazil last fall after working double shifts for several years. “My body couldn’t take it anymore. I couldn’t even take my feet off the ground.’’

Eventually, some of the employees summoned the courage to report Upper Crust to labor officials. That set off a firestorm at the chain.

Federal labor laws require employers to pay workers overtime, even if the workers are in the country illegally. The law is intended to dissuade companies from hiring such workers as a way to scrimp on payroll.

The Labor Department began its investigation in April 2009. Several months later, the gourmet pizza empire was ordered to pay nearly $350,000 in back wages to more than 100 workers, most of them immigrants from Marilac. Tobins said the company did not have enough cash to pay the arrears and was granted a 30-day extension, according to a copy of the compliance report filed with the Department of Labor and obtained by the Globe.