Cpl Wassef Ali Hassoun, 34, turned himself in and was being flown yesterday from an undisclosed location in the Middle East to Norfolk, Virginia.
He is to be moved today to Camp Lejeune in North Carolina, according to a spokesman, Capt Eric Flanagan.
Maj Gen Raymond Fox, commander of the 2nd Marine Expeditionary Force at Lejeune, will determine whether to court martial Hassoun.
Hassoun disappeared from his unit in Iraq's western desert in June 2004.
The following month he turned up unharmed in Beirut, Lebanon and blamed his disappearance on Islamic extremist kidnappers.
He was returned to Lejeune and was about to face the military equivalent of a grand jury hearing when he disappeared again.
Flanagan, said the Hassoun case is unrelated to the matter of Army Sgt Bowe Bergdahl, who disappeared from his post in eastern Afghanistan in June 2009 under unexplained circumstances.
Members of Bergdahl's unit have said he walked away on his own and should face desertion charges.
The Bergdahl case triggered a flood of controversy in part because of questions about the deal the US struck with the Taliban to gain his release May 31, after five years in captivity, in exchange for freeing five senior Taliban commanders from the US military prison at Guantanamo Bay, Cuba.
Bergdahl has not commented publicly on the circumstances of his disappearance and the Army has made no charges against him.
It is unclear where Hassoun, 34, has spent the past nine years after disappearing during a visit with relatives in Utah in December 2004. Nor is it known why he chose to turn himself in now. He was born in Lebanon and is a naturalised American citizen.