Federal agents have solved one mystery by learning the real identity of the man previously known as "John Doe," but now they're faced with...

Federal agents have solved one mystery by learning the real identity of the man previously known as “John Doe,” but now they’re faced with another, possibly more vexing question: Why has he repeatedly switched identities for the past 20 years?

Federal agents identified the man in custody in the SeaTac Federal Detention Center as Scott Andrew Shain, 52, who they say has adopted the identities of at least five dead people and obscured his past so well that it took federal agents nearly five months to determine his real name.

Positive identification came through the National Personnel Records Center in St. Louis, where records showed Shain was a former officer in the Air Force, said Special Agent Joseph Velling of the Office of the Inspector General with the Social Security Administration. That and other information the investigation turned up led to Shain’s parents in Illinois, who identified their son through photographs posted on the Web by the FBI, Velling said.

Shain was charged two weeks ago in U.S. District Court in Seattle with felony Social Security fraud, mail fraud and aggravated identity theft, but agents have been trying to figure out who he was — and what he was doing with his various identities — since November, according to court records. He was charged and arrested when it appeared he was about to adopt the identities of a deceased man and a teenage boy in Canada.

Agents are untangling a web of identities stretching back to the mid-1980s. They believe Shain has obtained dozens of driver’s licenses, Social Security cards and had at least two passports under other names.

Agents also are waiting for more information on his military history after Shain’s parents said he “fell off the face of the Earth” after he washed out of flight school, Velling said.

“He is a very intelligent guy,” Velling said. “He was in officer-candidate school. He was going to fly jets.”

Velling said the man’s family “said they’ve been dealing with this stuff in the past,” referring to a string of mostly fraud-related crimes that Shain or his aliases have been accused of over the years.

Federal investigators say Shain has apparently lived in New York, Massachusetts, Illinois, Wyoming, Idaho, Oregon and California. In 1983, Shain was living at Mather Air Force Base near Sacramento, Calif., according to records.

They also show that, between 1997 and 2004, he was listed as a resident at a home in Seattle’s Wallingford neighborhood.

During that time, according to court records, he was also known as Robert Allan Lowe (or Loew), William Gregg and William Gee.

When he was arrested, he had apparently been sleeping in a filthy, windowless 10-by 12-foot room in a run-down business on lower Queen Anne that he rented for $75 a month under the Lowe name.

Velling said agents executed a search warrant Monday on a computer seized in a search of that room, seeking to confirm information that Shain may have been involved in a Web site the agent described as “sort of eBay or Craigslist for criminals.” Assistant U.S. Attorney Johanna Vanderlee said the warrant was sealed.

Agents say the case has proved unusual because there has been little evidence that Shain was trying to use the identities for the sort of profit common with most identity thieves: obtaining credit and buying items in the name of the assumed identity.

One name he used is “Blake Matthew Desmond,” who has a warrant in King County for forgery issued in 1998.

And to complicate matters further, Velling said, it appears that Shain would sometimes adopt an identity and obtain Social Security cards and driver’s licenses in that name, only to go to court and have that name legally changed. He’s done that in Washington and Oregon, Velling said.

“Blake Desmond,” for example, used to be “Bernard O’Daly” in Boston — Shain’s hometown, Velling said. Shain apparently changed that name after moving West.

It’s under the Desmond identity that he was caught in 1998 trying to alter his fingerprints while applying for a concealed-handgun permit in Seattle.

According to Velling and evidence presented in court, Shain first attempted to obliterate the prints by painting a substance over his fingertips. When that failed, he used some sort of acid to try to burn them off.

He was caught and charged in King County Superior Court with perjury and giving a false statement, according to Velling and court records.

In 1993, Shain — using another identity — was interviewed by the Secret Service after making threats against then-President Clinton, Velling said. Agents found and confiscated a homemade flamethrower, according to federal prosecutors.

Mike Carter: 206-464-3706 or mcarter@seattletimes.com