In the days and weeks after he failed to report for duty in Kirtland, investigators found his vehicle at the Albuquerque International Airport.
Then just a few days ago, the mystery that began more than three decades ago came to an end.
His family feared that he had been abducted.
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There was even speculation that Hughes may have been abducted by or defected to the Soviets.
What do we know about Capt Hughes? He was expected to return to duty at Kirtland on August 1, 1983.
Checks with law enforcement around the USA and overseas, alongside interviews with those who knew Hughes, did not provide enough information for the Air Force to find him at the time. He will likely face charges of desertion.
"After being confronted with inconsistencies about his identity, the individual admitted his true name was William Howard Hughes Jr., and that he deserted from the U.S. Air Force in 1983", the AFOSI news release read.
Hughes, now 66, was taken into custody reportedly told investigators that he was "depressed" in the service and created a fake identity to start a new life. Hughes's disappearance, in the eyes of some, fit right into the puzzle.
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At the time of his disappearance, he was thought to have either been captured by Soviet agents or voluntarily defected to the Soviet Union, the Air Force Times reports. "These include the apparent defection to the Soviet Union in 1983 of the U.S. Air Force's leading expert on rocket self-destruct procedures" - meaning Hughes. One such anonymous official said, "He is worth his weight in gold to the Russians in terms of future 'Star Wars, ' if we have them".
The Albuquerque Journal reported that in 1984, the Pentagon had said that though he had top secret clearance, he did not have clearance that could "compromise national security". Although Hughes had access to "U.S".
However, Linda Card, a spokeswoman for the air force office of special investigations, told the Albuquerque Journal that investigators now see "no indication that he had any classified information or that he gave any classified information". But still, she said, the case remains under investigation.
"Until we have the whole story, we don't have the story", Ms Card said.
Hughes Jr. masqueraded as "Barry O'Beirne" for over 35 years after he deserted his post with the U.S. Air Force.
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Desertion carries maximum penalties of dishonorable discharge, forfeiture of all pay and confinement of five years.