Stephen Rakes, who was found dead in Lincoln on July 17, was buried on Thursday in South Boston.

He owned a liquor store that he said was taken from him in the 1980s by James "Whitey" Bulger, who stands trial for racketeering and murder. Rakes had waited decades to testify against the 83-year-old gangster, but his name was removed from the government witness list one day before he died.

An initial autopsy showed no signs of trauma, but police said they believe that Rakes' body had been moved, and that he died elsewhere.

The state medical examiner’s office is now conducting toxicology tests.

His funeral and wake earlier this week brought together friends and stirred up memories of South Boston from another era the good and the bad.

Listen 0:00 RAKES_FUNERAL_Mixdown_1%5B1%5D_1.mp3

At Spencer Funeral Home on Broadway in South Boston on Thursday, the Town had turned out to bid Stephen Rakes goodbye.

This was the old South Boston: an assembly of neighbors and friends who grew up together and hung out at familiar landmarks that dot this once insular community: Castle Island, Carson Beach, and Woody’s Tavern.

On the mantle as you entered the funeral home were dozens of photos of Rakes in his younger days; holding his infant daughters in his arms, flexing well-honed muscles at the L Street Bath House, and smiling for any and every camera.

Outside the funeral home, well wishers described the man they knew. William Fleming, a transit cop, said he had formed a strong bond with "Stippo" Rakes, 59, over three decades.

"He never touched drugs or alcohol too many people he knew had gone down that path and it had taken a toll on them," Fleming said.

Elise Orchard, who said Rakes was her son's godfather, suspected that Rakes was a victim of foul play.

"People in South Boston are not stupid, and we've gotten answers and we're gonna get them," she said. "We're gonna make people give... real answers."

The Middlesex District Attorney's office had no additional information on the cause of Rakes' death or the circumstances that preceded Stephen Rakes’s body being discovered on Mill Street in Lincoln on Wednesday, July 17. Police sources, however, are convinced that he died in a different location. Rakes' wallet was missing and so was his van. After a two day search, Rakes’ 1995 white Dodge Caravan was located in Waltham.

Several people saw Rakes the Tuesday after the government pulled him from a list of witnesses slated to testify against Bulger. He seemed distraught, they said. He had told me just days earlier how eager he was to take the stand to give his version of events explaining how his liquor store in 1984 ended up in the hands of Bulger, Stephen "The Rifleman" Flemmi, and the Winter Hill Gang.

One version of events came from Bulger’s former lieutenant, Kevin Weeks, who testified that Rakes voluntarily sold the store after receiving bomb threats. The store was a former gas station near the Old Colony housing project that Rakes and his wife Julie converted into a money-making business. Rakes maintained that he was forced to sell the store.

The U.S. Attorney's office removed Rakes from the witness list reportedly because prosecutors feared his testimony would contradict Kevin Weeks', thus undermining the government’s case against Bulger.

Rakes' friend Billy Fleming said he had spoken with Rakes two days before he disappeared. They spoke about the testimony he planned on giving at the trial.

"I just wish that he had gotten his day in court to take on the monsters that helped destroy this town," Fleming said.

When the law enforcement finally decided to move decisively against the so-called Irish mob in the 1990s, Rakes lied about the shakedown. In May 1996, he was indicted by a federal grand jury and charged with perjury and obstruction of justice.

Outside the funeral home, Rakes' attorney, Michael Connolly, said in those days Rakes distrusted the government more than he feared Bulger.

"He was convicted of perjury and at sentencing the government ... essentially gave him no penalty whatsoever," he said.

Rakes' ex-wife Julie sued the government for over $100 million for its use of informants that allowed Bulger to get away with taking the store, extorting, stealing, robbing and allegedly killing people. That suit, like almost every other civil complaint against the government for its role in abetting Bulger’s crimes, was thrown out by a U.S. judge.

Rakes went on to build a real estate business with mixed financial results. He came from a troubled family; his two sisters were caught up in drugs and The Life, his brothers were in and out of prison. One of them, Joseph, is the kid shown in the Pulitzer Prize winning photograph of a white teenager attempting to spear a black man in a suit and tie with the American flag during an anti-bussing rally downtown in 1976. The victim was Ted Landsmark.

Landsmark, now President of Boston Architectural College, went on to meet Joseph Rakes and to develop a friendship with his brother Stephen, who contacted Landsmark seeking to apologize for that incident nearly 40 years ago.

Rakes' friends describe him as complex, funny, resourceful and haunted by a personal history that has become a national story: the impact of Whitey Bulger on the Town.

On Wednesday night, Stephen Rakes, was dressed in a beige suit and matching tie as he lay in his casket at Spencer Funeral home. His son, two daughters and his girlfriend greeted dozens of visitors –an assembly of former co-workers, family, friends and South Boston neighbors.

They spoke in whispers and at times broke into loud laughter discussing how Stephen "Stippo" Rakes lived and leaving the questions of how and why he died ... to another day.