Oct. 25, 2011— -- Navy sailor Kyle Antonacci was found hanged last year while he was covertly helping an investigation that cleared another sailor of a rape accusation brought by a female Marine.
Antonacci's family, however, doesn't believe he committed suicide and fear he may have been murdered for his role in the investigation.
They also raised questions about how the Navy treated his death. The family says the Navy initially told them that Antonacci died in a car crash, and failed to tell them about injuries -- including a broken nose -- that their son suffered in his last moments. In addition, they claim that key evidence like investigation photographs of his injuries have disappeared.
"It's been hell," said Lisa Antonacci, the sailor's mother. "We feel like we are being completely ignored by the Navy. They took my son, put him in a box and that was that."
An ongoing, 20-month-long military investigation has yet to determine if Antonacci's death was homicide or suicide.
Lisa Antonacci said her son joined the Navy in hopes of one day becoming a SEAL, one of the country's elite special forces.
"He became intrigued with the Navy Seals," said his mother. "He didn't even like gym class, my son, but he wanted to be a Navy Seal. He said he wanted to make a difference and serve in the military."
So in 2007, Antonacci left his family's home in Long Island, N.Y., and moved to the Navy's largest training facility, 40 miles north of Chicago. Four years later, they face the excruciating task of unraveling their son's mysterious death.
In February 2010, Seaman Antonacci was found dead, hanging by a belt from his closet at Naval Station Great Lakes. His death, at age 22, was ruled asphyxia by hanging.
Navy Trying to Determine If Sailor's Death Was Suicide or Murder
Antonacci's parents believe their son's death is somehow linked to his undercover work with military investigators who were seeking additional information about a sex assault case.
The trouble began in 2009, when a female Marine accused Antonacci's friend Mike Pineda of rape. Antonacci gave testimony in that case that incriminated Pineda, although he did not actually witness a sexual assault.
After Pineda was convicted of aggravated sexual assault and sentenced to three months behind bars and given a bad conduct discharge from the Navy, Antonacci admitted he'd failed to tell the court that he had sex with the woman earlier on that same day -- a statement that could put her rape claim in question.
His parents say that is when the woman's friends -- all Marines -- began threatening their son.
"He said they carved an X on his door like a marked man," said his mother. "He was even threatened with a knife."
Pineda said, "I knew he had been threatened at least 10 times. Everybody knew it on base."
The Antonaccis said their son filed reports with his chain of command, begged the Navy for protection and asked to be moved off base.
Despite the alleged threats, Antonacci cooperated with investigators to help Pineda clear his name, according to sources familiar with the military's probe. Reports show that Antonacci phoned the female Marine involved in the rape case and allowed the Naval Criminal Investigative Service to record their calls, and ABC News has listened to one of the tapes.
Two hours after Antonacci made his last recorded call to the woman involved in the rape case, he was found dead in his room.
"They threatened Kyle. They told him they were going to kill him," said Pineda, who eventually had the charges against him dismissed and was granted an honorable discharge from the Navy.
"They could have moved him off base," Pineda said. "They could have moved him somewhere else. We share the barracks with the Marines. But no one did anything to help him."
Did Navy Hide Truth About Sailor's Death?
Antonacci's father, Al Antonacci, believes his son's death could have been prevented.
"If they had just taken him off base," he said, "I believe my son would be alive today."
A spokesman for the Naval Criminal Investigative Service would not comment on Antonacci's death or the alleged threats against him because its investigation is ongoing.
But from the beginning, the Antonaccis feel they have been misled. They say the Navy spokesman who came to their Long Island home to deliver grim news of their son's death initially said he had died in a car crash.
"It was a misdirection from the start," said Antonacci's father. "First, it was a car accident, then a massive aneurysm in his bunk."
Kyle's sister, Karissa Antonacci, finally contacted her brother's Navy colleagues via Facebook.
Said Antonacci's mother, "My daughter called me and said 'Do you want me to tell you how he died, or do you want the Navy to tell you?' She found out online."
Antonacci's family say they went on to learn even more disturbing information. According to the coroner's report, Antonacci suffered hemorrhaging around his face, a broken nose and other injuries the medical examiner said were "not consistent with a typical hanging."
The medical examiner wrote, "I was not 100 percent convinced this was a self-inflicted hanging."
Antonacci's parents were startled when they saw their son's body.
"He looked like he was tortured," said Lisa Antonacci, Kyle Antonacci's mother. "He had a giant black eye and scratches on his hands."
The Antonaccis say the were also told by the coroner's office that more than 100 photographs taken in the course of the autopsy had somehow vanished because of "technical problems."The coroner's report mentions that photographs were lost.
Six months after they buried their son, the Antonaccis paid tens of thousands of dollars to have his body exhumed. They hired famed medical examiner Dr. Michael Baden to conduct a second autopsy. Baden's autopsy discovered that -- Antonacci's hyoid bone, the only bone in the throat, which could provide crucial information as to how he died -- is missing.
Baden's report was inconclusive, in part because of the missing photographs and hyoid bone.
"We were desperate to know what happened to our son, and we have no answers," Antonacci's mother said.
Antonacci's mother says she isn't sure if her son was murdered or if all of the pressure and threats caused him to take his own life.
"I think he was either killed or bullied to death," she said. "The Navy didn't help him or protect him. He would have been safer in Iraq than he was in Illinois."