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WASHINGTON - An Iranian scientist sought refuge in the Pakistani Embassy compound and asked to go home, an apparent defection gone wrong that could embarrass the United States and its efforts to gather intelligence on Tehran's suspected nuclear weapons program.

Iran -- and at one point, scientist Shahram Amiri -- claimed the CIA had kidnapped him; the United States said Tuesday that nothing of the sort happened. Amiri disappeared while on a pilgrimage to Saudi Arabia in June 2009, surfacing in videos but otherwise out of sight until the latest bizarre twist in the case.

"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. It was the first time the Obama administration publicly acknowledged Amiri was in the United States.

Reliable and timely information about Iran's nuclear program is of enormous importance to the Obama administration and other countries seeking to stop the Islamic republic from getting the bomb. Beyond using diplomatic means to try to stop Iran, the United States and Israel have not ruled out using military force.

Iran maintains that its nuclear program is for peaceful purposes.

Washington has denied Iran's accusation that U.S. agents kidnapped Amiri, a charge that grew more confused with the appearance in recent months of videos purporting to show Amiri making conflicting claims about his fate.

"He left his family behind, that was his choice," said a U.S. official who was briefed on the case and spoke on the condition of anonymity because the official was not authorized to speak publicly about the case.

In one, he claimed U.S. and Saudi "terror and kidnap teams" snatched him; in another, he said he was happily studying for a doctorate in the United States. The murky circumstances gave credence to the theory that Amiri, 32, might have been coerced by Iran into claiming he was kidnapped.

"I expect they got to his family," said Clare Lopez, senior fellow at the Center for Security Policy and a former operations officer for the CIA. "Now he'll go back and save them." 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.

Whatever the reason for his disappearance, important questions remain about what of value, if anything, Amiri shared with American intelligence about the Iranian nuclear program.

State Department spokesman P.J. Crowley said he does not know what Amiri may have told U.S. officials, but he did say that the U.S. 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."

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."

In brief remarks to reporters, Clinton said it was up to Amiri to decide whether to stay in the United States.

"These are decisions that are his alone to make," Clinton said. "In contrast, Iran continues to hold three young Americans against their will, and we reiterate our request that they be released and allowed to return to their families on a humanitarian basis."

Clinton was referring to three American hikers who have been held by Tehran since July 2009 on an accusation of illegally entering the country. They have not been charged.

Clinton also mentioned the case of Robert Levinson, a former FBI agent who disappeared in Iran in 2007.

"We have asked Iran many, many times for information about his whereabouts, and we still do not have that information," Clinton spokesman Crowley said.

Michael Rubin, an Iran expert at the American Enterprise Institute, said he expects Iran to reap propaganda value from Amiri's return if he appears on Iranian TV to assert that he was kidnapped.

"What will happen now, however, is that the Iranians will score propaganda points, they will be able to televise a confession that may be more fiction than reality, but which regardless the CIA will have trouble refuting," Rubin said.

A Pakistani diplomat in Washington said Amiri arrived at a Pakistani Embassy office that handles Iran's interests in Washington at 6:30 p.m. EDT Monday. There he told Iranians that he had been dropped off by his captors. Clinton, though, said he intended to fly home Monday but merely had trouble making arrangements through transit countries along the way.

The Iranian interest section is technically part of Pakistan's embassy and is under Pakistani legal protection but is run by Iranians who issue visas for travellers to Iran and perform other functions.

The United States and Iran do not have formal diplomatic relations.

A video appeared on Iranian television on June 7. It showed Amiri speaking into what appeared to be a Web cam. He said the date was April 5, that he was in Tucson, Arizona, and that he was abducted in Saudi Arabia by U.S. and Saudi intelligence.

"When I became conscious, I found myself in a plane on the way to the U.S.," he said.

But a subsequent video appeared just hours later on YouTube on June 7. Amiri says into a camera that he is free, safe, happily living in the U.S. and working on his degree.

Yet another video appeared on Iranian TV on June 29. It shows Amiri saying the date is June 14.

"I have succeeded in escaping from American intelligence in Virginia," he said, adding that he was speaking from a "safe place" although he feared he could be rearrested.

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