Hughes Jr. masqueraded as "Barry O'Beirne" for over 35 years after he deserted his post with the U.S. Air Force.
There was speculation in the 1980s that Hughes, who specialized in space-launch command, control and communications for satellite surveillance systems, had defected to the Soviet Union, the Los Angeles Times reported in a July 1986 article.
Then his picture appeared on the news and TV satellite trucks showed up Monday on their quiet, tree-lined street in Daly City, just south of San Francisco, and it became clear their neighbor was not who they had thought. He was 33 years old.
A United States Air Force officer with top-secret clearance who deserted 35 years ago has been caught in California, where he has been living under an alias for more than three decades.
Hughes was last seen in the Albuquerque area withdrawing $28,500 from his bank account at 19 different branches, the Air Force said, though not indicating when.
Hughes was supposed to travel to the Netherlands in July 1983 to work with North Atlantic Treaty Organisation officers on the operations of AWACS electronic surveillance planes.
He is now being held at Travis air force base awaiting charges.
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It's unclear if he had an attorney who could comment on his behalf. In this photo, the Air Force Thunderbirds are seen rehearsing their precision flying routine, in Forestville, Maryland, Sept. 18, 2015.
He was officially declared a deserter on 9 December 1983, after interviews with friends and co-workers, and searches by law enforcement failed to give any clues about his location.
The Seattle Times reported in 1984 that the classification was made "primarily for administrative purposes".
At the time of his disappearance, he owned a house in Albuquerque.
"Capt. Hughes claimed that in 1983 he was depressed about being in the Air Force so he left, created the fictitious identity of O'Beirne and has been living in California ever since", the Air Force writes.
However, if an investigation finds Hughes leaked classified information - officials in the '80s initially anxious he might have defected or been involved in espionage - it would get a lot worse than a desertion conviction.
He was assigned to the Air Force Operational Test and Evaluation Center at Kirtland AFB, in New Meixco where his duties included classified planning and analysis of the North Atlantic Treaty Organisation command, control, and communications surveillance systems.
Checks with law enforcement around the US and overseas, alongside interviews with those who knew Hughes, did not provide enough information for the Air Force to find him at the time.