Iran’s Foreign Ministry said the scientist, Shahram Amiri, was on a flight home, traveling through the Gulf nation of Qatar and was expected to arrive in Teheran on Thursday.

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Iran ? and at one point, Amiri ? claimed the CIA had kidnapped him; the United States denied the allegation on Tuesday. Amiri disappeared while on a pilgrimage to Saudi Arabia in June 2009, surfacing in videos but otherwise remaining out of sight until he turned up at the Pakistani Embassy in Washington on Monday evening, asking to be sent home.

That prompted the Obama administration’s first public acknowledgment that Amiri had been in the United States. “Mr. Amiri has been in the United States of his own free will and he is free to go,” Secretary of State Hillary Rodham Clinton said.

While Iran has viewed the entire episode as an abduction, Amiri’s disappearance last year fueled reports that he had defected to the United States and was providing information on Iran’s nuclear program. The United States and its allies accuse Teheran of seeking to build a nuclear weapon, a claim Iran denies, saying its program is for peaceful purposes.

His return and a string of videos that emerged over the past month has raised questions. In one video that seemed to be made in an Internet cafe and was aired on Iranian TV, he claimed US and Saudi “terror and kidnap teams” snatched him. In another, professionally produced one, he said he was happily studying for a doctorate in the United States. In a third, shaky piece of footage, Amiri claimed to have escaped from US agents and insisted the second video was “a complete lie” that the Americans put out.

ABC News: Amiri missed his wife and son

ABC News reported that Amiri called home this year because he missed his wife and son in Iran and that his son had been threatened with harm.

A US official who was briefed on the case said Amiri, 32, “left his family behind, that was his choice.” The official spoke on the condition of anonymity because the official was not authorized to speak publicly about the case.

Before he disappeared, Amiri worked at Teheran’s Malek Ashtar University, an institution closely connected to the country’s powerful Revolutionary Guard.

State Department spokesman P.J. Crowley said he does not know what Amiri may have told US officials, but he did say that the US government “has maintained contact with him” during his stay in the United States. Pressed to say whether Amiri was a defector, Crowley replied, “I just don’t know the answer.”

On Wednesday, Iranian state TV aired part of a phone interview with
Amiri conducted a day earlier. He said that in the Saudi holy city of
Mecca, three men told him to get into a car, sticking a gun barrel
against his back. Amiri said the US had planned to hand him over to
Israel, which would release “false information against Iran” in his
name.

Deputy Iranian Foreign Minister Hassan Qashqavi told state TV that Iran
will pursue the case of Amiri’s abduction through legal means.

Iran’s foreign minister, Manouchehr Mottaki, told a news conference in
Madrid on Tuesday that Amiri was found after having been kidnapped
during the Saudi Hajj and taken to the United States against his will.
He demanded that Amiri be allowed to return home “without any obstacle.”