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RENEE MONTAGNE, host:

We're looking this week at America's clandestine war against Iran. We heard yesterday about sabotaging Iran's nuclear program in cyberspace. Today we look at the clandestine war in the physical world, where assassinations, bombings and defections have put added pressure on Iran's government. As NPR's Mike Shuster reports, it's a murky world where little is certain.

MIKE SHUSTER: Two years ago, Shahram Amiri, a young Iranian nuclear scientist, vanished in Saudi Arabia. For months nothing was heard of him. Then information surfaced that he had defected to the CIA and had provided the U.S. with crucial information about a secret nuclear site in Iran. Last year Amiri undefected. He surfaced, declared he had been a prisoner of the CIA and wanted to go home. And so he did.

Professor PAUL PILLAR (Georgetown University): The Amiri case seems to be a story out of the wilderness of mirrors department.

SHUSTER: Paul Pillar is a former senior CIA official who now teaches security studies at Georgetown University.

Mr. PILLAR: In which intelligence agencies and the services and governments against which they operate are constantly in uncertainty about just where the loyalties of the people they're dealing with ultimately lie.

SHUSTER: Amiri was believed to be an agent-in-place for the CIA, who then decided he wanted out of Iran. In the U.S. it appears he got cold feet and made his way back to Iran. There he was initially hailed as a hero. Months later he was jailed. Now he is on trial for treason.

There was one other known defection back in 2007. Ali Reza Asgari, a senior military officer, disappeared in Turkey. Nothing else is known for certain about his case. He may be in the U.S., possibly in Israel. It is likely he provided valuable intelligence to both nations.

The CIA is looking for human sources of intelligence in Iran all the time. Karim Sadjadpour, an Iran specialist at the Carnegie Endowment for International Peace, believes there could be many more cases still in the shadows.

Mr. KARIM SADJADPOUR (Carnegie Endowment for International Peace): When you have a regime which is deeply unpopular, it makes the covert war in some ways more enticing, because it's easier to recruit disaffected officials within the Iranian system.

SHUSTER: After the disputed 2009 presidential election and the brutal crackdown on opposition demonstrators, recruitment may have become even easier for intelligence agencies from the U.S. or Britain or Israel, says Reuel Marc Gerecht, a former CIA agent, now with the Foundation for Defense of Democracies.

Mr. REUEL MARC GERECHT (Foundation for Defense of Democracies): It may have been the great turning point for people who were revolution-loyal to suddenly look upon the CIA or MI6 or Mossad as a legitimate way to express their opposition to the regime.

SHUSTER: The clandestine war against Iran is not free of violence. Killings and bombings have occurred, although infrequently. Last fall, two scientists connected to Iran's nuclear program were the targets of car bombs in Tehran in broad daylight. One was killed, the other survived.

Several months before that, another young nuclear engineer, Massoud Ali Mohammadi, was killed when a booby-trapped motorcycle exploded. Iran blamed the U.S. and Israel, but that might not be the whole story, says Karim Sadjadpour.

Mr. SADJADPOUR: In the case of Ali Mohammadi, you had an individual who was connected to Iran's nuclear program who the intelligence ministry had raided his home, who was thought to have an affinity and ties with the Iranian opposition. The next day he was killed in a very public, brutal fashion.

SHUSTER: The bombs have not been confined to Tehran. For many years there has been small-scale violent resistance to the Iranian government, usually carried out by ethnic minority groups far from the center. There have been bombings in Iran's Sunni southeast, in Baluchistan, attributed to a group known as Jundullah; and in the southwest province of Khuzestan, an oil-rich area dominated by Arab-Iranians, several bombs went off there just recently.

The Iranian government always blames the British or the Israelis or the Americans for these attacks. That could be true, says Paul Pillar, but it doesn't have to be.

Mr. PILLAR: We're talking about individual elements of opposition to the regime, of which there are a good number. A bombing can take place as the work of a small group or cell that on its own initiative decides to cause problems for the regime.

SHUSTER: Tension with ethnic minorities in Iran is widespread, with many feeling disaffected from the central government, notes Karim Sadjadpour.

Mr. SADJADPOUR: There's ample reason why they should feel disaffected and ample reason why you would see, expect to see agitations among the population. So I don't think that they need the United States or certainly Israel to encourage them to agitate. They have plenty of reasons themselves for wanting to have a greater political and economic voice.

SHUSTER: Still, that doesn't exclude the possibility that local cells receive outside support. Last year the leader of Jundullah claimed his group had been financed and trained by the CIA. But he made that claim in a public confession on Iranian state TV after he had been captured. Then he was executed.

All part of the wilderness of mirrors that is the clandestine war against Iran.

Mike Shuster, NPR News.

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MONTAGNE: We wrap up our series tomorrow with a look at covert operations that are part of U.S. policy toward Iran.

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MONTAGNE: This is NPR News.

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