Before leaving New Mexico, Hughes withdrew $28,500 from his bank account, making smaller withdrawals by visiting 19 different branches, the Air Force said.
A U.S. Air Force captain with top security clearance has been arrested 35 years after he walked away from his job and was declared a deserter by the defense department.
Hughes is awaiting pretrial proceedings for his desertion case at the Travis Air Force Base in Fairfield, Calif.
"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 U.S. Air Force in 1983", the USAF said in a statement.
Military.com reported that Hughes was found due to a passport fraud investigation.
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. He had been at Kirtland since 1981, working on highly classified operations involving NATO's command, control and communications surveillance systems, according to the news release.
Before he mysteriously disappeared and landed on the Air Force Most Wanted list, Capt. William Howard Hughes Jr. phoned home to tell his mother and father that he was going to the Netherlands.More news: Gmail for Android Gets Customisable Swipe Actions With Latest Update
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Agents from the Air Force's Office of Special Investigations took Hughes into custody at his California home Wednesday, the Air Force said. Hughes was recently apprehended 35 years after he is alleged to have deserted.
At the time of his disappearance, Hughes was in his early thirties.
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.
Military officials said Hughes had access only to secret information pertinent to North Atlantic Treaty Organisation.
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.
"Until we have the whole story", she said, "we don't have the story". Hughes may also forfeit all pay that he received while he was part of the Air Force.
Hughes faces desertion charges, which carries a maximum of five years in prison.