When Seaman Kyle Antonacci was found dead in his barracks room in early 2010, it looked like a suicide. His family, however, suspected foul play.

Antonacci, a 22-year-old explosive ordnance disposal trainee then assigned to Naval Station Great Lakes, Illinois, had been embroiled in a perjury investigation at the time of his death. It stemmed from a rape case in which he had been a key prosecution witness. He later admitted he had failed to disclose that he, too, had sex with the woman that night, information that could have affected the outcome of the case.

Although the Naval Criminal Investigative Service did not properly conduct its investigation into his death, according to a report from the Defense Department Inspector General's Office released Oct. 28, there was no evidence that those mistakes led investigators to a wrong conclusion about how he died or that there was a conspiracy to rule his death a suicide.

The report also called out NCIS' poor handling of the rape case and subsequent perjury investigation.

In October 2011, friends and family of Antonacci told the Deerfield (Illinois) Patch that they believed NCIS' handling of the case contributed to Antonacci's death. They believed — in part because officials gave them multiple explanations of how the seaman died — that he was killed because of his involvement in the rape case.

The DoD IG report, however, stood by the medical examiner's conclusion that Antonacci's death was a suicide, asphyxia by hanging.

Antonacci's family did not respond to multiple phone calls seeking comment over a month. An independent forensic pathologist who autopsied Antonacci declined to comment without the family's permission.

The report is the latest in a series of black eyes for NCIS, which in the past has been accused of mishandling multiple sexual assault cases and has taken steps to improve its investigative procedures.

"NCIS cooperated with the DoD IG during its review of this matter, and we are taking steps to address the recommendations made," NCIS spokesman Ed Buice told Navy Times.

The IG opened an investigation after an anonymous tip to find out whether the three investigations had been properly carried out.

On the day he died, Feb. 1, 2010, NCIS interviewed Antonacci as part of its perjury case after he came forward to say he had lied about what happened the night of the alleged rape. According to NCIS procedure, he should have been released to his command, but instead he went back to his room alone.

The NCIS agent let Antonacci go because he or she considered him a "cooperating defendant" in the case, rather than a "confessed military suspect," which requires release to the chain of command, according to the report.

Antonacci was found dead there three hours later, the report said.

The first investigation

The story began in May 2009, when a female Marine lance corporal reported she had been raped by a Navy E-3 in Antonacci's room at the naval station.

Antonacci knew the victim and the alleged perpetrator, Seaman Michael Pineda, according to a 2013 Los Angeles Times report; he'd been casually dating the Marine, and Pineda was a good friend.

The three had been partying that night, and the drunk, 21-year-old Marine had gone looking for Antonacci, who called Pineda to "help him deal with her," the story said.

Both men had sex with her the night of May 8, and the Marine later accused Pineda of rape. He was convicted of having sex with someone too drunk to consent, sentenced to three months in jail and dishonorably discharged from the Navy, the LA Times reported.

He won an appeal in 2011, upgrading his discharge to honorable and awarding back pay for the remainder of his service obligation, the LA Times reported.

The IG found that the initial rape investigation hadn't met NCIS standards, starting with the case reviews.

It's procedure is to review cases every 30 days, but at the time of the November 2009 court-martial, the case had only been reviewed three times, rather than the five required since it was opened in May.

The IG also found that the interviews weren't thorough. NCIS only interviewed two witnesses who knew what the victim had been doing the night of the reported rape, though she provided the names of several potential witnesses. One of them was Antonacci.

The alleged assault took place in his room and Antonacci was the first person to talk to the woman afterward, but NCIS waited 20 days to interview him, the report said. The questions were also inadequate.

"More thorough questioning may have developed information that SN Antonacci's last sexual encounter with the victim occurred on May 9, 2009, the same evening as the rape," according to the report.

The only other witness interviewed spoke to NCIS 70 days after the initial report, according to the IG.

More botched investigations

In September 2009, Antonacci reported he'd been threatened by a male Marine — a friend of the victim's — after the victim accused him of "switching sides" in the case because he had told an acquaintance that he didn't think Pineda was guilty of rape.

NCIS did not open an investigation, the IG report said, though the male Marine later admitted to confronting Antonacci and carving an "X" into his barracks room door a week before the seaman was found dead.

It took three years for NCIS to investigate the threat, presenting the male Marine's testimony and photographic evidence of the carving to Navy and Marine Corps officials in November 2013.

The IG found fault with the perjury investigation initiated after Pineda had been found guilty.

In December 2009, an unidentified witness accused Antonacci of lying by not disclosing his sexual relationship with the victim. According to the witness, Antonacci admitted to having sex with the woman that night, before the rape took place.

On Jan. 19, 2010, NCIS brought Antonacci in for interrogation.

"Antonacci stated he was not truthful in his testimony because he thought, based on a conversation between him and the victim, she would accuse him of rape if he did not testify on her behalf during the court-martial," the report said.

Over the next week, he came in multiple times for questioning, an NCIS-monitored call to the victim and a polygraph test. On Jan. 28, the case agent called Antonacci's command to discuss the seaman's alleged "suicidal ideations," suggesting he may have needed a suicide watch.

When interviewed, the officer-in-charge at the time said he didn't recall that discussion.

On Feb. 1, Antonacci called the victim a second time, again with NCIS agents listening in. The victim said she didn't remember having sex with him on the night of the reported rape.

Following the call, according to the report, Antonacci went back to his room and "informed a close friend that his life was over and he was going to jail."

The friend went to check on him soon after, finding Antonacci hanging by a belt around his neck in his closet.

The case agent working with Antonacci told the IG that he arranged for a command escort following each of his meetings with the seaman, but there was only documentation for one of them, on Jan. 29. He couldn't explain why he hadn't written anything down about the others, he told investigators.

There was some disagreement among NCIS agents over whether Antonacci was considered a "confessed military suspect," as the case agent deemed him to be, and whether he needed an escort. The supervisory special agent thought he was a "cooperating defendant," according to the report.

Finally, NCIS mishandled the investigation into Antonacci's death as well, the IG found.

First, NCIS didn't interview the two agents overseeing the perjury investigation, though they were two of last people to speak to the seaman before his death.

They also didn't follow up with a witness with whom Antonacci's had chatted online before his death, in which he referred to serving in the Navy as "suicidal bad," the report stated.

After the Lake County, Illinois, coroner ruled the death a suicide, Antonacci's family hired a private forensic pathologist to look at the body again.

According to the LA Times, the pathologist found that Antonacci's body was bruised and his nose bloody, which weren't consistent with someone who had hanged himself. The Lake County coroner said his nose made a grating sound when moved, like it might have been broken, but the private pathologist described it as intact.

Further, the coroner said a bone in Antonacci's throat was intact during the first autopsy, but the pathologist said the bone wasn't present at all.

NCIS did not re-interview the coroner and private pathologist to clarify the discrepancies, the IG found.

However, the report stated, those differences didn't matter in the larger scheme of things, because the Office of the Armed Forces Medical Examiner still ruled the death a suicide.

The IG recommended NCIS beef up training for supervisors and agents, and clarify the meaning of "confessed military suspect."

Meghann Myers is the Pentagon bureau chief at Military Times. She covers operations, policy, personnel, leadership and other issues affecting service members. Follow on Twitter @Meghann_MT

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