His duties included classified planning and analysis of North Atlantic Treaty Organisation command, control and communications surveillance during the Cold War.
But, after completing a tour of duty in the Netherlands and spending two weeks on holiday in Europe, Capt. Hughes vanished.
He had just completed a stint in the Netherlands, where he worked with North Atlantic Treaty Organisation officers on the Airborne Warning and Control electronic surveillance aircraft. The Air Force didn't say where in California Hughes had lived under the O'Bierne name, or what charges he faces.
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.
Last week, almost 35 years after he went missing, the Air Force finally found Hughes living in California under the fictitious name "Barry O'Beirne". Inside his townhouse they discovered a to-do list and a list of books Hughes planned to read upon his return.
" 'We do not feel he disappeared voluntarily, ' his sister, Christine Hughes, said in the article". Others speculated that he had defected -possibly to the Soviets - with the highly classified information, a notion that fomented conspiracy theories for years.
The U.S. State Department was investigating Hughes - who claimed to be "Barry O'Beirne" - for possible passport fraud when he revealed his true identity.
Hughes reportedly returned to New Mexico on leave in July 1983.
He told authorities after his capture Wednesday that he was depressed about being in the Air Force and made a decision to leave.
However, Linda Card, a spokeswoman for the air force office of special investigations, told the Albuquerque Journal that investigators now see "no indication that he had any classified information or that he gave any classified information".
Last year, there was uproar when Bowe Berhdahl was spared prison time after being found guilty of deserting his Afghan outpost - instead he was reduced to private in rank, dishonourably discharged and lost pay. Friends and co-workers also didn't provide any information, the Air Force said.
But AFOSI spokeswoman Linda Cardsaid there are many more questions to be answered as the investigation continues.
In 1986, three years after his disappearance, journalist Tad Szulc wrote a piece published in the Los Angeles Times that referred to Hughes' "apparent defection" to the Soviet Union.
Hughes has been charged with desertion and is being held at Travis Air Force Base in California.
"Until we have the whole story, we don't have the story", Ms Card said.