The evidence that finally brought criminal charges against Whitey Bulger came to investigators by chance, and it had been languishing in file cabinets for over ten years before it was used. In 1983, the Massachusetts State Police bugged Heller's Café in Chelsea, believing that it was a "bookmakers' bank" where checks from losing gamblers were cashed and money was laundered. Bookies from all over the Boston area congregated there to conduct business, and state police investigators listened in on conversations that revealed the inner workings of an enormous illegal gambling operation. According to the Boston Globe, they learned that Michael London, the owner of Heller's, washed $50 million a year, and ace oddsmaker Burton "Chico" Krantz took in over a million dollars a week. But along with the hard information about the illegal gambling industry, the investigators also heard some very interesting shop talk, particularly the bookies' gripes about having to pay rent to either the Mafia or Whitey Bulger and Stephen Flemmi. None of them liked the situation, but nearly all of them complained about it, and the state police got it all down on tape. It was solid evidence that Bulger and Flemmi were extortionists.

The bookies were rounded up, and the U.S. Attorney's office came up with a unique strategy for putting their feet to the fire. In addition to charging them with illegal gambling, the bookies from Heller's Café were charged with money-laundering. Instead of the expected legal slap on the wrist, the bookies were now facing the possibility of long sentences in federal facilities. One by one, they began to make deals with the government, offering to cooperate in ongoing investigations against organized crime in Boston in exchange for leniency.

Years later, in August 1990, 51 individuals involved in a Southie cocaine ring were charged as a result of a 15-month DEA investigation. Bulger was not charged, but members of his crew were. True to their Southie roots, Bulger's henchmen refused to snitch on their boss, but the indictments exploded the myth that Whitey Bulger kept drugs off the streets of South Boston.

Around this time, Tim Connolly, the mortgage broker who had been threatened at knifepoint by Bulger and waylaid by the FBI, went to the U.S. Attorney's office out of desperation. Fearing for his life, he offered to wear a wire and testify against Bulger.

Little by little, over a period of nearly twelve years, authorities gathered enough evidence to charge Bulger, Flemmi, and Boston Mafia chieftain "Cadillac Frank" Salemme with racketeering and extortion. Authorities decided that all three would be arrested simultaneously, fearing that they would flee if they learned that any one of them had been apprehended. Unfortunately, the arrests didn't play out the way the authorities had hoped. On January 5, 1995, Flemmi was taken into custody without a glitch, but it took seven months to find Frank Salemme in Florida. Bulger disappeared completely.