The Air Force Office of Special Investigations said in a news release this week that William Howard Hughes, Jr., was apprehended at his home after a fraud investigation involving a fake identity he had been using.
In fact, just a day before Hughes' arrest, the man was interviewed by the State Department's Diplomatic Security Service over possible passport fraud, detailed the Air Force Times.
This undated photo released by the U.S. Air Force shows Capt. William Howard Hughes, Jr., who was formally declared a deserter by the Air Force Dec. 9, 1983.
Hughes was unmarried when he disappeared, but the Seattle native had three sisters.
After the Air Force formally declared Hughes a deserter in December 1983, his family said in an Associated Press article printed in the Journal on January 20, 1984, they believed he had been abducted.
Hughes apparently lived in California under the assumed identity of Barry O'Beirne.
He allegedly told investigators that he became depressed while serving in the Air Force so he left and created a new identity for himself.
William Howard Hughes Jr. was formally declared a deserter by the Air Force on December 9, 1983.
At the time of his disappearance he had just returned from the Netherlands, where he had been working with North Atlantic Treaty Organisation officers.
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He was supposed to be back in Albuquerque by August of that year. Others speculated that he had defected -possibly to the Soviets - with the highly classified information, a notion that fomented conspiracy theories for years.
The Air Force classified Hughes, who had a "Top Secret/Single Scope Background Investigation" clearance, as a deserter a few months later.
"We do not feel he disappeared voluntarily", his sister, Christine Hughes, said in a 1984 Associated Press article, according to USA Today.
In the years after Hughes went missing, a slew of NASA catastrophes, such as the space shuttle Challenger disaster of 1986, as well as the explosion of the Ariane rocket in French Guinea, caused national security commentators to speculate whether the disasters were related and possibly the result of Soviet sabotage.
He faces a maximum sentence of five years confinement, forfeiture of all pay and dishonourable discharge for his desertion.
After several rocket ship failures in the United States and France, including the Challenger space shuttle disaster in 1986, Los Angeles Times journalist Tad Szulc theorised Capt Hughes may have been to blame.
Mr Szulc also said an intelligence officer told him Capt Hughes was "worth his weight in gold to the Russians in terms of future "Star Wars".
"They (AFOSI investigators) said at this point there's no indication that he had any classified information or that he gave any classified information..."
"Until we have the whole story, we don't have the story", she told the newspaper.