William Howard Hughes Jr., who disappeared in 1983 and was living under an assumed name in California, was discovered this month after a passport fraud investigation found inconsistencies with his identity, according to CNN.
He has been living under the alias Barry O'Beirne since then.
Air Force Capt. William Howard Hughes Jr. started at Kirtland in 1981, working on NATO's command, control and communications surveillance systems.
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, a Seattle native was arrested without incident on Wednesday.
Interviews with Hughes' friends and associates and inquiries with law enforcement agencies in the United States and overseas failed to locate him, the statement said, and he was formally declared a deserter on December 9, 1983.
Hughes' neighbors in Daly City, California, told CNN he went by the name "Tim" and that he lived with a woman they said they believed to be his wife.
At the time of his disappearance, the Air Force said Hughes had a "Top Secret/Single Scope Background Investigation" clearance. He was last seen in New Mexico withdrawing $28,500 from his bank account at 19 different branch locations, the Air Force said in a statement.
It was July 17, 1983, and the Air Force was sending Hughes overseas on a mission to help North Atlantic Treaty Organisation test aircraft surveillance systems.
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Hughes was assigned to temporary duty in the Netherlands, working with North Atlantic Treaty Organisation to test its new Airborne Warning and Control System, created to be used for surveillance, command and control, battle space management and communications.
Hughes was due back in Albuquerque in August at the time he vanished, and on December 9, 1983, the Air Force formally declared him a deserter.
In a 1984 article by the Associated Press, Capt Hughes' family said they believed he had been abducted. Hughes was charged with desertion.
A spokeswoman for the Air Force Office of Special Investigations told the Albuquerque Journal there's no sign Hughes leaked classified information or was involved with the Soviet Union, but that investigations are underway. Others speculated that he had defected -possibly to the Soviets - with the highly classified information, a notion that fomented conspiracy theories for years.
Later in 1986, a Los Angeles Times article also speculated that Hughes had defected to the Soviet Union.
Hughes faces desertion charges, which carries a maximum of five years in prison.
"He is worth his weight in gold to the Russians in terms of future 'Star Wars, ' if we have them", the LA Times quoted an intelligence officer as saying. An OSI spokesperson told the newspaper that there was no indication Hughes had given away any classified information.
"Until we have the whole story, we don't have the story", Ms Card said.