RENEE MONTAGNE, host:

The U.S. is publicly involved in three wars - in Iraq, Afghanistan and in Libya. This morning we'll hear about a fourth - a covert war - against Iran.

STEVE INSKEEP, host:

This conflict does not involve casualties on a battlefield, but the stakes are high. The U.S. has been trying to stop or slow down Iran's nuclear program.

MONTAGNE: On the surface, President Obama's administration has used diplomacy, first reaching out to Iran and then tightening sanctions when that failed.

INSKEEP: Below the surface, the U.S. has become involved in cyber-attacks, encouraging defections, and more. NPR's Mike Shuster begins a series on these activities with a look at U.S. sabotage.

MIKE SHUSTER: Covert action is meant to stay just that - covert, clandestine, in the shadows. And in Iran, it did for quite some time.

But in the last year, much has become known about intelligence operations in Iran, says Bruce Riedel, a former CIA official, now an analyst with the Saban Center at the Brookings Institution.

Mr. BRUCE RIEDEL (Brookings Institution): There's little doubt that there's a covert war under way against Iran. There are at least two players in it: the United States and Israel.

SHUSTER: And often, it appears, those players work together.

That was especially true with the Stuxnet worm. This is a computer virus -apparently developed in Israel with the help of the CIA - that was launched in 2009. Sometime the following year, the worm found its way into the computers that control Iran's most important nuclear facility, the uranium enrichment operation at Natanz.

It told the gas centrifuges that enrich uranium to spin too fast. Many broke and destroyed other centrifuges - nearly a thousand of them.

The impact of the worm spread even wider than that, says Muhammad Sahimi, a professor at the University of Southern California, who writes for the website Tehran Bureau.

Professor MUHAMMAD SAHIMI (University of Southern California): In fact, not only it destroyed a thousand centrifuges at Natanz, it also forced the government to actually shut down the enrichment facility for a few days.

SHUSTER: That was last year. Computer security companies got wind of it, in part because it may have also affected companies and equipment outside of Iran. And the story became public.

Computer security experts believe the original worm was programmed to mount multiple attacks. That may have occurred, but only up to a point, says David Albright, director of the Institute for Science and International Security in Washington.

Mr. DAVID ALBRIGHT (Institute for Science and International Security): This idea of multiple destruction was built into the planning of the program, and Iran thwarted it just by the simplest of steps, which is panic and shut down everything until you get a sense of what's going on.

ALLEN: Given the success of the Stuxnet worm, it's likely its creators may be constructing Stuxnet 2.0 right now, or other viruses targeting Iran.

Iran may have had to buy new computers to replace those that were affected, and it can't be sure that new computers won't be sabotaged. In fact, nothing that Iran buys on the international market that could be used in its nuclear program is safe from sabotage, says Muhammad Sahimi.

Mr. SAHIMI: To say the least, probably the uncertainty whether there is a virus somewhere that they haven't detected, that causes a lot of problems for them.

SHUSTER: Among those problems, the Russians who are finishing the Bushehr nuclear reactor - Iran's first - stopped their work to ascertain whether it had been infected with the worm. And this worm isn't the first instance of sabotage, says David Albright.

Mr. ALBRIGHT: It's one of many efforts that I think are under way to try to constrain Iran from being able to basically, in a sense, either outfit its centrifuge program or to try to actively disrupt it and break things.

SHUSTER: Among the parts of the centrifuges that have been sabotaged, according to Albright, are motors and vacuum pumps. Inspectors from the International Atomic Energy Agency discovered equipment at Iran's nuclear facilities that had passed through one of the U.S. national laboratories, Albright says.

Mr. ALBRIGHT: So you had a case where the U.S. government, at least, what it was doing was buying equipment on the open market and then apparently modifying it in some way.

SHUSTER: Then the equipment was apparently delivered to front companies that in turn sold it to Iran. It could have been used for sabotage, or if it was bugged equipment, it could provide information on the location of secret nuclear facilities in Iran.

In any case, Iran's leaders are certainly worried about what they might face next, says Bruce Riedel.

Mr. RIEDEL: One of the benefits of these kind of programs is that over time it builds paranoia and fear inside the Iranian nuclear program, that they have to be extremely careful that anything they buy may turn out to be a self-destructive pill once it's ingested inside the Iranian program.

SHUSTER: In fact, in late April one of Iran's key nuclear officials disclosed that another computer virus had hit Iran. The Iranians are calling it the Stars virus. They say they've taken care of it.

So far, computer security specialists outside of Iran have not determined its nature. Nevertheless, the effort to sabotage Iran's nuclear program, through cyber-attacks or other methods, is certain to continue.

Mike Shuster, NPR News.

MONTAGNE: And tomorrow we'll hear about defectors, assassinations and homemade bombs.

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