This story originally aired on April 18, 2009. It was updated on Oct. 24.
In the spring of 2005, Air Force Colonel Philip Michael Shue was laid to rest at Arlington National Cemetery with full military honors.
Shue was 54 when a violent car crash took his life two years earlier. His vehicle struck some trees alongside a Texas interstate highway, not far from San Antonio.
But even as his widow, Tracy, accepted the traditional tri-folded American flag in his honor and even as she left a single white rose on his casket in his memory, she and those closest to him spoke of one final mission for truth.
"Phil, know this. That while you rest, the mission for truth will continue and it will be accomplished," his cousin, Ron Shue said at the service.
It all began 15 years before, in 1988, when Tracy, then an Air Force nurse, was assigned to Eglin Air Force Base in Florida.
"I liked him. I like him as a person. He was a great doctor… everybody loved him," Tracy tells "48 Hours Mystery" correspondent Troy Roberts.
Tracy and Phil, a psychiatrist, soon began dating. Phil was separated and was going through a difficult divorce.
"He didn't talk a lot about his first wife other than to say there was not any love in the marriage," says Tracy.
In 1993, with the divorce finalized, Phil and Tracy decided to marry. Tracy says they had a great life together.
"I don't think in my whole life I have ever met somebody who had such passion for life and just enjoyed the simple things," she tells Roberts. "He just -- he would walk into a room and he would just light it up. And people loved him. He brought nothing but joy into my life. I was very happy."
Five years later, in 1998, Phil was reassigned to Lackland Air Force Base in San Antonio, Texas. He and Tracy bought a house in nearby Boerne.
Nina Willard is Tracy's nearest neighbor, and her closest friend.
"Well, Phil had that Midwestern, very low-key, soft-spoken - mild-mannered, very laid back. And Tracy was a born and bred New Yorker, a little bit more demonstrative, I guess, you could say," she says with a laugh.
The friendship developed over the next five years of Phil and Tracy's marriage. Willard had mixed feelings in 2003, when Phil decided to retire from the Air Force. "Well, we were sad to see 'em go," she says.
Phil and Tracy had already found their dream house in Alabama -- a big place, with a pond in back.
"It was a new adventure. A new chapter in his life," Tracy says. "I mean, life was just very, very exciting at that moment."
Just one day after putting down a deposit on their new home, early on the morning of April 16, 2003, the colonel dressed in his fatigues and brought Tracy her customary first cup of coffee.
"We had coffee in bed - typical morning. [A] normal day, other than he was getting to work a little early to do some paperwork," she recalls. "We sat there and talked. We talked about the house. And he kissed me goodbye and left and said, 'I love you.' And those were the last words he said."
Two hours later, Col. Shue was dead.
"That car caved in on the driver's side and he suffered major head trauma as a result and was apparently killed instantly," explains Lieutenant Roger Anderson, who saw pretty quickly that this was more than a car crash.
"They could see that the T-shirt underneath had been ripped open from the chest to the naval. There was a 6-inch vertical gash in the man's chest and that both nipples had been removed," he says.
Anderson says there was another very unusual set of findings.
"They could see on his right wrist what appeared to be duct tape… both wrists actually were wrapped with duct tape in the similar way, both dangling ends. There was also duct tape at the top of his boots," he explains.
It would take a year of investigation, but in time, all of the agencies involved - the local and state police, even the Air Force - would come to agree that the death of Col. Philip Shue, a psychiatrist, was actually the end result of his own bizarre psychological breakdown: a deeply disturbed Shue had committed suicide.
"The case is bizarre," says Dr. Vincent Di Maio, who was the chief medical examiner of Bexar County, Texas. His office performed the autopsy.
Read the findings of the Bexar County, Texas Medical Examiner's Office
Of any knowledge of Phil Shue's emotional state in the weeks leading up to his death, Di Maio says, "The information that was provided to the office was that he had been having some problems. He had seen some of his colleagues for depression or panic attacks."
Di Maio believes the injuries found on Shue's chest are self inflicted.
"You believe that Dr. Shue mutilated himself and went to these bizarre lengths to commit suicide?" Roberts asks.
"Well, based upon the information that was provided, that's the only conclusion," Di Maio replies.
The district attorney convened an investigative grand jury - 12 citizens sworn to secrecy - and asked them to consider the case.
"The grand jury found no evidence of any crime, and believed that the ruling of suicide should stand," says Anderson.
Tracy Shue is determined to prove her husband did not commit suicide, but, in fact, was murdered.
"I couldn't allow such an injustice to have happened not only to a wonderful person, but a person that I loved," she says.
Of the duct tape on her husband's wrists and ankles, the excised nipples and the gash in his chest, Tracy says she believes that Phil had been abducted and tortured. "What other explanation could there be?"
But if Shue had been kidnapped and then bound and tortured, and then somehow managed to escape, Di Maio wonders, why didn't he seek help?
"I mean, if you had been tortured like that, and you had broken free, where would you go? You would go to either the police or a hospital. But he was driving away from San Antonio and the hospitals. He passed three of the exits to his own town, Boerne. He had a working cell phone. I mean, this action is not consistent with someone fleeing an assailant."
"There's just no way," says the Shue's neighbor, Nina Willard. "He wouldn't have done that. He wouldn't have done it to Tracy."