A former operations manager at Upper Crust has filed a lawsuit that accuses the Boston-based pizza chain of retaliating against him after he reported the company to the US Department of Labor for allegedly violating wage and hour laws. Patrick Joyce claims Upper Crust's owner, Jordan Tobins, falsely accused him of robbing the Commonwealth Avenue store, docked his final paycheck by hundreds of dollars, and threatened to kill him, according to a copy of a complaint filed in US District Court in Boston. Joyce worked at Upper Crust for seven years. He is seeking about $150,000 in damages, said his lawyer, Elayne N. Alanis. 'Initially, it was a business with good intentions,' Joyce said. 'I think greed and arrogance got in the way. ((Tobins)) was blinded by his own arrogance. As the company grew and his stardom grew, he felt he could do whatever he wanted.' George Regan, a spokesman for Upper Crust Pizzeria, said the allegations are not true. Joyce is 'angry that another employee received a promotion,' Regan said. 'He was not threatened, he was reprimanded for poor performance - not for being a whistle-blower. His version may sound more glamorous, but it is not true.' Upper Crust, which rapidly expanded over the past decade to 17 stores, has come under scrutiny by several state and federal agencies for its treatment of workers, many of whom arrived illegally in Boston from a village in Brazil. Joyce's lawsuit is the second this year brought by former employees. In July, two former cooks filed a lawsuit saying the popular pizza chain took back thousands of dollars in overtime payments that were ordered by the Department of Labor. The federal agency investigated Upper Crust's pay practices in 2009 and required it pay nearly $350,000 in back wages to about 121 employees. After making the restitution payments, management allegedly demanded the Brazilian immigrants surrender their overtime checks or lose their jobs. The two former cooks claim in court records that Upper Crust began drastically reducing weekly paychecks to recoup the federally ordered payouts, and then fired them. The company, through Regan, has disputed all of the allegations. 'We appreciate our employees and are responsible for keeping more than 250 people in Massachusetts employed, thus we must run our business professionally,' Regan said. In his suit, Joyce said he told Tobins's business partner, Brendan Higgins, and general manager Barry Proctor that employees were routinely working in excess of 70 hours a week at a flat rate of $455, without any overtime pay. In January, Joyce contacted the Labor Department and detailed what he believed to be illegal or unethical practices. The agency recently confirmed it has launched a new investigation. In May, Joyce said, Tobins accused him of being involved in a robbery at one of the company's restaurants and launched into a 'tirade of obscenities,' according to the suit. In response, Joyce said, he resigned. Regan, in a previous interview, said the company did not allege that Joyce was involved in a crime. 'If the company thought Mr. Joyce was implicated in the theft, he wouldn't have remained with the company,' Regan said. After discovering in June that several hundred dollars were missing from his final paycheck, Joyce said, he told Tobins he would report Upper Crust to the Labor Department if the money was not returned. According to the suit, Tobins responded by saying 'I will ((expletive)) kill you.' Joyce filed an incident report with the Boston Police Department in July that included the same accusations: 'Mr. Joyce feels that he is being targeted and is in fear of his safety because people from his company believe he went to the Department of Labor as well as the press to open up this investigation,' the report said. 