Chambersburg Police Detective Dianne Kelso launched an investigation.
"It looked very suspicious at the outset," said Franklin County Coroner Kenneth L. Peiffer.
Thompson's hands were handcuffed in front of him, he had a dog collar around his neck and roller skates on his feet, Peiffer said. It was all tied together with ropes, Peiffer said.
He was found lying on his back, his head resting on two plastic jugs and his feet resting on a mattress where he had slept.
But Thompson's death Wednesday afternoon turned out to be an accident, Peiffer said.
An autopsy Thursday revealed that Thompson died of auto-erotic asphyxia, Peiffer said.
Kelso could not comment on the cause of death Thursday because she had not yet seen the autopsy report.
A Pennsylvania State Police fire marshal's investigation has determined the slow, smoldering fire was probably accidental, Kelso said.
Thompson used candles for light, Kelso said.
Thompson's friends described him as a nice man who was trying to find a job and an apartment.
He had been sleeping in the storage garage on and off for the last year or two, they said.
"We had no idea that anybody was staying here," said garage owner Ray Kegerreis, inspecting fire and smoke damage to three of the 11 units on Thursday.
Thompson rented the small garage for $45 a month. It has no utilities and the lease prohibited anyone from sleeping there, Kegerreis said.
The Barges family said they often gave Thompson meals and let him use their shower.
"He was very nice, kind man. He was very loving," said Wanda Barges of Chambersburg, who brought flowers to the storage garage on Thursday.
Barges' husband, Jimmy, and his seven brothers all tried to help Thompson.
"I was his best friend," said Roy Barges, who complained that Thompson couldn't get any government assistance.
The Franklin County Assistance Office and Human Services Department said confidentiality rules prevented them from saying whether Thompson had applied for their help.