Exclusive: Iranian Nuke Scientist Is En Route to Iran

Iranian defector Shahram Amiri

The CIA has lost one of its most valued former spies.

Iranian nuclear scientist Shahram Amiri, who defected to the US, is now on his way back home to Tehran after a very messy and public re-defection.

ABC News obtained exclusive photos of Amiri leaving Washington's Dulles International Airport late Tuesday night on a commercial flight to Doha, Qatar, en route to Iran.

Amiri was escorted directly to the jetway entrance by a security officer. He was flanked by what appeared to be a U.S. official and a representative from the Pakistani Embassy in Washington._He boarded the Qatar Airways flight ahead of the other passengers, and spoke only to his companions.

After more than a year in the US, Amiri claimed he had never really defected. In a series of videos released on the internet, he insisted that he had been kidnapped, drugged and tortured by the CIA.

The US flatly denies that it ever held Amiri against his will.

"Let me say that Mr. Amiri has been in the United States of his own free will," said Secretary of State Hillary Clinton. "And he is free to go."

Clinton said that Amiri was actually scheduled to travel to Iran on Monday "but was unable to make all the of the necessary arrangements to reach Iran through transit countries."

U.S. officials tell ABC News that Amiri defected in the spring of 2009 after working for several years for the CIA while still inside the Iranian nuclear program.

But officials say that after Amiri was re-located to Tucson, Arizona he began to have second thoughts.

In a battle of videos posted on YouTube, first by the Iranians and then the CIA, Amiri changed his story three times.

First, he told Iranian TV via computer phone he had been kidnapped.

Then, in a CIA-produced video, Amiri said he was happy to be in the US.

Later, he again claimed he was trying to elude US agents so he could be reunited with his wife and son in Iran.

"In case anything happens to me or if I do not make it back home safely, the responsibility will solely rest on the officials of the United States," Amiri said in one of the videos.

CLICK HERE and HERE TO SEE AMIRI'S MOST RECENT VIDEOS IN ENGLISH

"This happens all the time," said Bob Baer, a former CIA officer who worked in the Middle East. "Defectors come up with a good idea to make a lot of money, and then once the boredom sets in and the loneliness, they want to get back in touch with the family. They realize it was a huge mistake."

Amiri Leaves for Iran, Americans Still Held by Iranians

On Monday evening Amiri showed up in Washington, DC at the Iranian interest section of the Pakistani embassy. Because the US and Iran do not have full diplomatic relations, Iran does not maintain its own embassy in Washington.

Before his flight home, Amiri told Iranian television he had finally escaped from the hands of US intelligence, something US intelligence officials say he had to say to avoid being imprisoned or executed upon his return to Tehran.

"If they want to keep up the pretense that he was kidnapped," said Baer, "I think they'll probably keep him alive. I think they'll give him a couple of years as a public hero. After that I can't tell you."

CLICK HERE to follow the ABC News Investigative Team's coverage on Twitter.

The case of the returned defector allows the US to again ask Iran to release the three young American hikers it is holding as spies, as well as to raise the issue of former FBI agent Robert Levinson, who has been missing in Iran for three years.

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