Capt Hughes was living under the name Barry O'Beirne, but investigators unravelled his story after spotting inconsistencies and he later admitted his real identity. In his home, the investigators found lists of plans and books he wanted to read, the article states.
In December 1983, Air Force officials declared Capt. Hughes to be a deserter.
Captain William Howard Hughes Jr was last seen on 25 July 1983, when he withdrew a total of $28,500 (£21,300) from 19 bank branches around Albuquerque, New Mexico, where he was stationed following his return from service in Europe. He was expected to return to duty at Kirtland on August 1, 1983.
His mysterious disappearance during the Cold War spurred theories that he had been abducted by the Soviet Union or defected to what was then known as the USSR to work against the US.
The reason he did this, he said, was because he was "depressed about being in the Air Force" - so he left, created a fictitious identity in California and never came back, investigators said. Hughes was arrested at his residence without incident June 6 on charges of desertion, the Air Force Office of Special Investigations announced in a news release Thursday.
Card said Hughes' family has been notified of his apprehension, but it is unknown whether they had been in contact with him or knew his whereabouts.
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.
At the time of his disappearance, Hughes was in his early thirties.
"Intelligence officers believe that Hughes was either captured by Soviet agents or voluntarily defected to the Soviet Union", the Times said.
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".
The Seattle native's family refused to accept the Air Force's declaration and said they believed their loved one had been abducted. Secret and NATO Secret information, " the Air Force maintained that he was not carrying classified information with him on his trip to the Netherlands. But still, she said, the case remains under investigation.
Linda Card, a spokeswoman for the Air Force Office of Special Investigations, told the Albuquerque Journal Sunday that to this day officials still do not have any evidence indicating leaks of classified information. "Until we have the whole story, we don't have the story".
He is now being held at Travis Air Force Base in California, faced with charges of peacetime desertion, which is punishable by up to five years in prison.
Desertion carries maximum penalties of dishonorable discharge, forfeiture of all pay and confinement of five years.
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