He had been last seen in New Mexico, where he withdrew almost $30,000 from his bank account at 19 different branch locations.
Mystery has surrounded the discovery of a high ranking Air Force Officer with top secret clearance who went missing more than 35 years ago only to 'apparently' re-surface in California.
A man who deserted from the US Air Force in July 1983 has been apprehended in California, the US military says.
The Air Force said it declared Hughes a deserter December 9, 1983.
TaskandPurpose reported Hughes' auto being found at the Albuquerque airport and a search of his home in the 1900 block of Chandelle Loop NE revealed notes of planned activities and books to read upon his return.
Hughes was involved in classified planning and analysis of North Atlantic Treaty Organisation control, command and communications surveillance systems during the cold war. Prior to his "capture", Hughes had been formally declared a deserter by the Air Force Dec. 9, 1983. Others speculated that he had defected -possibly to the Soviets - with the highly classified information, a notion that fomented conspiracy theories for years.
Hughes said he had been depressed about being in the Air Force so he deserted, made up the O'Beirne identity and moved to California, the Air Force said.
In a news release, the Air Force Office of Special Investigations (AFOSI) said the Department of State was investigating a man named "Barry O'Beirne" in connection to a passport fraud inquiry.
He has been living in California under a fake identity ever since his defection. Hughes's disappearance, in the eyes of some, fit right into the puzzle.
Later that year, the unmarried Seattle native was declared a deserter - something one of his sisters refused to believe.
"He is worth his weight in gold to the Russians in terms of future 'Star Wars, ' if we have them", Szulc quotes an unidentified intelligence officer as telling him.
He had a Top Secret/Single Scope Background Investigation clearance, which meant he had access to US and North Atlantic Treaty Organisation secret information. Friends and co-workers also didn't provide any information, the Air Force said.
An office of special investigations spokeswoman told the Albuquerque Journal that there was no indication Hughes was involved spying for or passing information to the Soviet Union or that any classified information was leaked.
Hughes, now 66, has been charged with desertion.
"Until we have the whole story", she said, "we don't have the story".