The former commander of Naval Station Guantanamo Bay, Cuba, was indicted this week for allegedly misleading investigators about the circumstances leading up to a man’s death there four years ago.

Capt. John R. Nettleton, 53, was indicted on several counts of obstruction of justice, making false official statements, falsifying records and other alleged infractions tied to the early 2015 death of Christopher M. Tur, a civilian Navy Exchange employee on the island.

Nettleton is not charged in Tur’s death. Instead, the indictment focuses on the days after Tur disappeared following what authorities suspect was a violent fight with Tur after a party.

Investigators allege that Nettleton stonewalled subordinates, superiors and investigators during a search for the missing man.

Nettleton’s attorney, Marine veteran Colby Vokey, told Navy Times by email that Nettleton was “innocent of these charges” and “is looking forward to the opportunity to finally being able to rebut the allegations and the investigations after having this hanging over his head for several years.”

The scandal began when Tur confronted Nettleton during a boozy Hail and Farewell party at the Bayview restaurant on Jan. 9, 2015, and accused the CO of having an affair with his wife, who was director of the Fleet and Family Support Center, according to the indictment.

Later that night, Tur and Nettleton battled at Nettleton’s house. Tur was injured in the altercation and was found dead and floating in the island’s waters a few days later, prosecutors wrote in the court filings.

An autopsy showed Tur had drowned “but he also had ribs that were fractured with associated soft tissue damage, and that these rib injuries occurred before he died,” the indictment states.

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“The autopsy also found that Tur had a laceration on his head.”

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A paper towel with blood on it that matched Tur’s DNA was found near the pier in Nettleton’s backyard after the death, the indictment states.

Naval Criminal Investigative Service agents searched Nettleton’s house on Jan. 20, 2015, and located bloodstains on the first floor that matched Tur’s DNA, too.

The Navy fired Nettleton as base commander the next day and he’s been assigned to Navy Region Southeast in Jacksonville, Florida, since then, according to service records.

A spokesman for the command did not return a request for comment about Nettleton’s current duties.

Navy Times also extended to Nettleton, through his command, a chance to give his side of the story but he never called.

Attempts by Navy Times to call his cell phone and home number also were unsuccessful.

Although NCIS probed Tur’s disappearance and death, it remained unclear Wednesday why Nettleton’s indictment was filed in the civilian U.S. District Court, Middle District of Florida, and he wasn’t charged in the military criminal justice system.

Navy officials referred questions to the Justice Department, which did not respond to requests for comment.

Navy Capt. John R. Nettleton holds his salute after he tossed a commemorative wreath into the bay during Naval Station Guantanamo Bay's 2014 ceremony remembering the Battle of Midway. He's since been indicted for lying to authorities about a scandal there. (Department of Defense)

Tur moved with his wife and kids to Guantanamo Bay in 2011 and was the NEX’s loss prevention safety manager at the time of his death, according to the indictment.

The base commander since 2012, Nettleton attended a farewell party in a basement section of the Hangar Bar at the Bayview for a departing executive officer.

Nettleton, Tur and Tur’s wife were all at the party, “and each consumed several alcoholic drinks,” according to the indictment.

“During the party, Nettleton and Tur’s Spouse spent time near one another in view of other party guests, including Tur,” the indictment states.

At about 10 p.m., “Tur yelled at Nettleton and Tur’s Spouse, accusing them of having an extramarital affair," according to the court filings.

The XO urged Nettleton to leave, and he headed to his residence, which was on the same road as the bar, prosecutors allege.

It appears as if Tur followed him. Tur spoke on the phone after 10:30 p.m. with a civilian resident on the base, referred to only as “K.W.” in the indictment.

Tur told the person that he was “at the Skipper’s house” and that he “just knocked the Skipper out,” according to the filing.

“K.W. also heard Nettleton stating words to the effect that Tur had ‘just knocked him out,” the indictment states.

Nettleton’s daughter, identified only as “J.N.,” heard noises downstairs, came down “and observed her father lying on the ground,” according to the indictment.

She saw a man, “who she eventually realized was Tur,” standing near her father, so she returned to her room and messaged friends about the incident: “Um well my dad’s really drunk and some other dude is here and they’re like getting into a fight downstairs and I’m hiding.”

“So um now I can hear them fighting really loudly omh (sic) I’ve locked myself into my room,” she said in another message to a friend.

“So um I like texted my brother and told him what was happening bc I could still here [sic] them fighting and [the dog] was barking at them and I didn’t know what to do and he tried calling dad like six times and he didn’t answer, and I could hear dad answer the phone downstairs and things have been quiet since then,” she said in another message.

Nettleton later emerged, shirtless; he spoke to his daughter and then went to bed, prosecutors wrote.

Early the next morning, an unnamed civilian and sailor started searching for Tur, who never returned to his home.

They went to Nettleton’s residence and he told them that Tur "had spoken with him, but that Nettleton told Tur to leave and Tur did,” the indictment states.

“Nettleton did not state that there was a physical altercation between himself and Tur or that Tur had been injured.”

View of Cooper Field at Naval Station Guantanamo Bay, Cuba as seen from John Paul Jones Hill. (Mass Communication Specialist 2nd Class Kegan E. Kay/Navy)

The sailor asked permission to look in Nettleton’s backyard, “which Nettleton refused to grant,” according to the indictment.

That afternoon, Nettleton told the base command duty officer to start searching for Tur, but he failed to reveal that he had a public argument with him that ended in a fight: “When asked by (the command duty officer) where to search, Nettleton said the last place Tur had been located was the Bayview,” the indictment states.

That’s why the dragnet continued north, south and east of the Bayview “but not west towards Nettleton’s residence, where Tur had actually last been seen by Nettleton,” prosecutors wrote.

A sister military law enforcement agency to NCIS, Criminal Investigative Division, opened a missing person case.

“However, without information about Tur’s accusations at the Bayview on Friday night or his appearance at Nettleton’s residence and the physical altercation there, CID investigators did not question Nettleton or take other steps to focus their missing person investigation on Tur’s presence at Nettleton’s residence and Nettleton’s knowledge of the circumstances surrounding Tur’s disappearance,” the indictment states.

Also that day, Nettleton informed a captain identified as “C.G.” that a search was underway for a missing civilian, but he failed to share any details about the affair accusations, the fight or that Tur was last seen at his house, according to the federal filing.

NCIS agents opened their own investigation that day, and again Nettleton failed to provide them with all the information about his involvement with Tur, the indictment alleges.

On the evening of Jan. 10, 2015, Nettleton ordered the entire command duty office to search for Tur and sent an email to a superior — identified in the indictment as “Admiral M.J.” — about the developing situation.

At the time, Vice Adm. Mary Jackson was the head of Navy Region Southeast, the command that oversaw Naval Station Guantanamo Bay.

“We are searching for an NEX employee, [Tur], he was last seen at the O’Club around 0100, and may have walked to the Marine Hill mini mart (based on charge card info) some time after that,” Nettleton wrote. “Alcohol is a factor and this has happened before, never for this long though. We are preparing for the worst and hoping for the best, Chaplains ready if needed.”

In the email, Nettleton noted that Tur’s spouse was the Fleet and Family Support Center director for the base.

Nettleton wrote back to the admiral and said Tur’s spouse “said he got physical with her at the bayview (sic) which is why she left,” the indictment states.

Nettleton also approved a so-called “Navy Blue” message that indicated Tur was last seen leaving the Bayview, authorities say.

“At no point on or about January 10, 2015, did Nettleton inform Admiral M.J. or any of his superior officers or subordinates that…Tur had accused Nettleton outside of the Bayview of having an extramarital affair with Tur’s Spouse, that Tur had later come to Nettleton’s residence after the party, that Tur and Nettleton had engaged in a physical altercation that left Tur injured, and that Nettleton knew the last place Tur had been seen by anyone was Nettleton’s residence,” the indictment states.

The next morning, Nettleton refused to let his XO request a Coast Guard helicopter to help search for Tur.

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After a phone call with the admiral later that day, Nettleton told his XO that the flag officer “did not need to know” about what had gone down at the Bayview, the indictment alleges.

At about 11 a.m. on Jan. 11, 2015, Tur’s body was found in the water “drifting westward and nearing the territorial water border with Cuba,” prosecutors wrote.

A few hours later, people still searching for Tur “discovered a paper towel, with a reddish-brown stain on it, near the base of the pier in Nettleton’s backyard,” according to the indictment.

“Nettleton was nearby when one of the Navy personnel recovering the item stated that it appeared to have blood on it,” the indictment states.

“That’s probably nothing,” Nettleton said but it later matched Tur’s DNA, according to the filing.

The Navy’s Inspector General received an anonymous complaint on Jan. 12, 2015, alleging that Nettleton and Tur’s spouse had an affair “and were engaging in physical contact at the Bayview during the Hail and Farewell party.”

Nettleton told an unidentified captain there was “absolutely no truth to this rumor,” the indictment states.

“I was not having an affair,” he said. “None of this is going on.”

But “Nettleton knew that he and Tur’s Spouse had engaged in an extramarital affair in or about 2014,” the indictment states.

On Jan. 13, 2015, Nettleton finally fessed up to the admiral about the Bayview party, and how “there was a lot of drinking at this event and there had been an argument between Tur and Tur’s Spouse inside the event and also in the parking lot,” the indictment states.

He told the admiral about Tur coming to his house but didn’t mention the fight and denied rumors of an affair.

The admiral told Nettleton to take this information to NCIS, but he never did, according to the indictment.

The next day, Nettleton told a captain that he withheld details about the incidents preceding Tur’s death because “I just didn’t think it was particularly relevant,” the indictment quotes him as saying.

Tur’s widow also denied having an affair with Nettleton when questioned by NCIS officials.

“Tur’s Spouse informed Nettleton of what she told NCIS and Nettleton responded ‘good,’” the indictment states. “Tur’s Spouse told Nettleton she thought her relationship with Nettleton was ‘none of their business,’ and Nettleton agreed.”

He kept in touch with Tur’s wife and said he was worried about being sent to court-martial for adultery.

“Tur’s Spouse also said that in the event there was a court-martial proceeding, she would refuse to appear and provide testimony, which Nettleton said was ‘good to hear,’” the indictment states.