FAIRFIELD (CNN) — A US Air Force officer with top-secret clearance who went missing in 1983 has been living under an assumed name in the Bay Area, according to the Air Force Office of Special Investigations.

Capt. William Howard Hughes Jr. disappeared in July of 1983 after returning from duty in Europe. 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.

Interviews with Hughes’ friends and associates and inquiries with law enforcement agencies in the US and abroad failed to locate him, the statement said, and he was formally declared a deserter on December 9, 1983.

Then just a few days ago, the mystery that began more than three decades ago came to an end.

“On June 5, during a passport fraud investigation, the US Department of State’s Diplomatic Security Service interviewed an individual claiming to be Barry O’Beirne. After being confronted with inconsistencies about his identity, the individual admitted his true name was William Howard Hughes Jr., and that he deserted from the US Air Force in 1983,” the Air Force said.

“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.”

Special agents from Travis Air Force Base took Hughes into custody at his California home Wednesday and he is being held at the base, the Air Force said. It is unclear what charges he faces.

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. The neighbors said he was a friendly guy who loved the San Francisco Giants, and that they were all stunned by the news of his past.

Neighbor June Dayao told KPIX 5 Hughes had lived in the Daly City neighborhood south of Serramonte with his wife Anna since 2010.

“I feel really bad for Anna,” said Dayao, who described Hughes as “very quiet, unassuming.”

Other neighbors offered descriptions of Hughes that told a similar story.

“Friendly, pleasant,” said area resident Michael Tom. “I guess you never know a person unless you really dig deep.”

“Best neighbor a guy could ever have,” said neighbor Lorenzo Laurel.

The Air Force said that Hughes had a “Top Secret/Single Scope Background Investigation” clearance at the time of his disappearance.

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.

In 1985 and 1986, several French and American rocket ships failed to launch properly and subsequently exploded, including the Challenger space shuttle. In the wake of those disasters, Los Angeles Times journalist Tad Szulc reported in July of 1986 that intelligence officers believed the rockets may have been sabotaged with Hughes’ help.

“(Intelligence officers) see a clear link between Hughes and possible sabotage of the American and French launches,” the newspaper reported then.

“He is worth his weight in gold to the Russians in terms of future ‘Star Wars,’ if we have them,” one intelligence officer told the Times.

Hughes’ sister, Christine Hughes, told the Associated Press in a January 1984 article that the family believed he had been abducted, according to the Albuquerque Journal.

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