The war is under way, though no one declared it and no one will confirm it. This is the secret war against Iran's nuclear project. It did not start this week or last month. It has been under way for years, but only faint echoes have reached the public.

In June 2010, the press reported that the computer system operating the uranium enrichment centrifuges at Natanz had been infected with a virus. A deadly worm, known as Stuxnet, had infiltrated the controllers, manufactured by Siemens.

Open gallery view Credit: Alon Gaash

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Two weeks ago, a huge blast ripped through a Revolutionary Guards military base 40 kilometers west of Tehran. The explosion could be heard as far away as the capital. Dozens of people were killed, including the head of Iran's missile development project, General Hassan Tehrani Moqaddam. This week, there was a powerful explosion in Isfahan, Iran's third-largest city, which has a uranium conversion plant on its outskirts. It is not yet clear what was damaged in the blast.

These incidents involved three key elements of Iran's nuclear program. The first is uranium conversion (which comes after the mineral has been mined ), the second is enrichment, and the third is the delivery means.

Coupled with other incidents, including the assassination of several Iranian nuclear scientists, these events have worried the ayatollahs' regime, causing reactions ranging from embarrassment to anger. The public response usually follows a pattern: first a sweeping denial, then a limp and stuttering admission that "something happened," and finally the claim that it was an "accident." This shows that the regime does not know exactly what to say, and that its voice is not uniform. It also reflects the fierce dispute within the regime's top ranks. The leadership is divided, and the reactions come from a range of ministries, rival organizations and competing media outlets.

The kind of sabotage used in Iran requires sophistication, financial and technological resources, agents and precise intelligence. Someone, for example, had to know that General Moqaddam would be at the base that day to supervise a test, apparently of a new missile engine.

Infecting the computers required access to them: A person with a flash drive had to have plugged it into the system. The prevailing assumption is that foreign intelligence agencies are initiating, managing and executing the secret operations.

The Iranians, and international media outlets, believe these operations are the work of Israel's Mossad and possibly also a Western partner such as the CIA or Britain's MI6.

The Mossad's campaign to assassinate the Black September members behind the 1972 Munich Olympics massacre was code-named "Wrath of God." This week, when asked whether God had carried out the recent operations in Iran, former Mossad head Meir Dagan smilingly said yes. Dagan is known to be an ardent supporter of secret operations, as he told Yedioth Ahronoth explicitly this week. He believes it will be at least two years until Iran can assemble a functioning nuclear weapon. This assessment may be based on past secret operations and on Dagan's faith that future actions can indeed disrupt Iran's progress.

A senior American official went even farther. President Barack Obama's special assistant and coordinator for arms control and weapons of mass destruction, proliferation and terrorism, Gary Samore, said in May 2011, "I'm glad to hear they are having troubles with their centrifuge machines, and the U.S. and its allies are doing everything we can to make it more complicated." Do we need any clearer statement that humans are behind the "hand of God"?

Even if the Mossad or the CIA are not involved in these incidents, the speculation that they are serves Western intelligence bodies by enhancing their image as "omnipotent," and heightening the Iranian leadership's fear. This is known as psychological warfare.

Still, with all due respect for Western intelligence's great efforts - including what is probably unprecedented operational coordination - it is unlikely these operations could have succeeded without inside support, meaning from individuals or groups ready to help sabotage the ayatollahs' regime. It should be remembered that Iran is a mosaic of ethnic minorities, and almost all have reasons for disliking the regime; some have their own underground armed militias.

The theory about inside-help gains traction given that, in addition to the military targets, other sites - including oil facilities, gas pipelines, trains and military bases - were also damaged over the past year. Last year there was a considerable increase, of at least 10 percent, in "breakdowns" and "accidents" at Iran's strategic infrastructure sites. Some were caused by poor maintenance, due in part to the international sanctions, but the volume of these incidents may also indicate the "hand of God" was involved. If this is the case, then it's possible that internal Iranian opposition groups (as opposed to exiles ) are stronger and even better organized than generally thought.

It is almost certain that Tehran's patience is about to run out. This was evidenced by the student mob's "conquest" of the British embassy this week. This was not spontaneous rage: It was a warning from a regime that realizes someone has declared war on it without leaving marks or fingerprints.

Sooner or later, the ayatollahs' regime will decide to react and will order its secret intelligence and operational units to retaliate. If and when this happens, Iran will take steps to conceal its involvement in such activities. However, past experience proves that despite the caution and sophistication of the Iranian secret services, they have often failed in obscuring their fingerprints.

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