The Twilight War: The Secret History of America's Thirty-Year Conflict With Iran

by David Crist

  Despite the election disturbances, Obama still held out hope for a deal on the Iranian nuclear impasse. In August 2009, Iran allowed IAEA inspectors into its nearly completed Arak heavy-water reactor and allowed expanded monitoring of its Natanz facility, which produced all of Iran’s enriched uranium. That fall, Iran asked the IAEA for help finding fuel for the small U.S.-built Tehran research reactor, which produced radioisotopes for medical use that treated about ten thousand patients a week. Supplies were slated to run out by the end of 2010. Working with the IAEA, the United States brokered an agreement for Iran to ship about 80 percent of its stockpile of low-enriched uranium to Russia, where it would be further enriched and eventually turned into fuel and sent back to Iran. The agreement was a concession by Washington in essentially acknowledging Iran’s right to enrich its own uranium, even if it was turned into fuel rods elsewhere. At the same time, the United States surprised and embarrassed Iran by publicly exposing the existence of a secret nuclear facility being built at Qom.

  Under the pressure, it seemed the two sides had achieved a breakthrough. Iran formally accepted the deal in principle, setting the stage for a face-to-face meeting between U.S. and Iranian negotiators. On October 1, the chief American diplomat, Undersecretary of State William Burns, met with Iranian negotiator Saeed Jalili. The two met for forty-five minutes during a break for lunch during the P-5 plus one talks in Geneva, with each side raising its concerns: the nuclear weapons program and human rights issues for the Americans; a worldwide ban on all nuclear weapons and access to peaceful nuclear energy for the Iranians. Afterward, Jalili called the discussions “good talks that will be a framework for better talks.” It all appeared encouraging. Iranian president Ahmadinejad publicly backed the deal, calling it a step forward that paved the way for the future.15

  President Obama expressed guarded optimism. “We’re not interested in talking for the sake of talking. If Iran does not take steps in the near future to live up to its obligations, then the United States will not continue to negotiate indefinitely.” In discussions with the Europeans, the president looked to the end of the year for progress on Iran; if this deal fell through, Obama would not abandon diplomacy, but he intended to turn to the stick of sanctions.

  With so much at stake, Iran did an about-face and reneged on the deal. By constitutional design, the Iranian government was fractured into competing centers of power. Still reeling from the presidential election upheavals, the government simply could not make a decision on such a significant issue. The supreme leader distrusted the populist and secular Ahmadinejad and felt no inclination to accommodate the West. Ahmadinejad’s other detractors within the regime were also not inclined to hand the president a victory, and they conspired to scuttle the agreement. As John Limbert, who headed the Iran portfolio at the State Department, commented about the collapse of the deal: “It was clear that serious divisions existed in Tehran. They could not come to an agreement among themselves.”16 One Iranian diplomat expressed the sentiment differently. “Just because the negotiation team agree to terms does not mean that the government will. But before we could decide in Tehran the Americans and Europeans were already pressing for sanctions. That was not the way one showed mutual respect.”17

  In his annual Nowruz speech the next spring, Obama began, “I said, last year, that the choice for a better future was in the hands of Iran’s leaders. That remains true today.” He then continued, “Faced with an extended hand, Iran’s leaders have shown only a clenched fist.”18

  So Obama turned to the UN Security Council and took a page from his predecessor’s book. On June 9, 2010, the council passed Resolution 1929, the fourth round of sanctions against Iran. These new sanctions targeted Iran’s military by banning the sale of weapons to Iran and freezing the assets of the Revolutionary Guard, and targeted both individuals and institutions involved in developing Iran’s ballistic missile program.

  On December 6, 2010, the United States again sat down across the table from an Iranian delegation in Geneva. In preparation, the State Department had drawn up a list of items for discussion, including Iran’s continued support of Shia militias attacking U.S. forces in Iraq. The United States would be prepared to discuss these and other issues of importance to Iran, provided the nuclear issue was first on the agenda.

  However, the Iranian negotiator Saeed Jalili wanted to discuss everything but the nuclear issue. He proposed forming a series of working groups to explore the various issues dividing Iran and the West. William Burns countered that the United States would agree to support this only if Iran’s nuclear program was addressed first. William Burns concluded that these working groups would offer the perception of cooperation, but would avoid making any actual decisions, which is what Iran wanted all along. The United States delivered a message to Jalili that Iran needed to take practical steps to build confidence in the peaceful nature of its nuclear program, or else the sanctions would continue. At the end of the talks, a State Department memo summed up the American view: “Iran’s performance was disappointing and unconstructive.”

  While the president had not given up on diplomacy, he increasingly concluded he needed to rely on other options to curtail Iran’s nuclear program. General Cartwright believed that, short of an invasion and occupation of Iran to overthrow the regime, Iran would not stop its nuclear program. He told this to President Obama in one of their first meetings on Iran. The president did not like the prospect, but he soon came to the same realization. Cartwright understood Iran’s nuclear rationale. “They don’t have much of a conventional military. The cheapest path they have to getting their sovereignty assured is a nuclear path,” he said.19

  Cartwright, the Joint Staff’s point man for formulating Iran policy, met with Israeli officials to discuss a way forward against Iran. In Bush’s second term, Israel and the United States had discussed joint operations to undermine Iran’s program. Israeli officials proposed extreme measures such as assassinations of Iranian scientists and supporting armed opposition groups inside Iran. Washington completely rejected these schemes, but within the limits of American legality the two nations developed common plans to derail Iran’s nuclear program as well as interdict arms transfers to Hezbollah and into Iraq. After a rough start between the Obama administration and Israel over Jewish settlements in Palestine, the two nations renewed efforts at cooperation to thwart Iran’s mastery of nuclear enrichment even if the two allies had mismatched policies and were frequently at odds. As one 2009 memo noted, “For us, suspension of enrichment is a means to an end. For Israel, it looks to be an end in itself.”

  Other nations quietly agreed with the idea of a covert campaign to halt Iran’s nuclear program. In January 2010, Volker Perthes, director of Germany’s state-funded Institute for Security and International Affairs, told U.S. officials in Berlin that undercover operations would be “more effective than a military strike” in curtailing Iran’s nuclear ambitions. In a memo leaked to the British media from WikiLeaks, he noted that “covert sabotage (unexplained explosions, accidents, computer hacking, etc.) would be more effective than a military strike whose effects in the region could be devastating.”20

  The role of cyber warfare took on a new importance. The U.S. military established a new four-star command called Cyber Command to carry out military operations in the computer battlefield. According to newspaper accounts, before leaving office, President George W. Bush had approved $300 million for projects aimed at delaying Iran’s nuclear program. The New York Times reported that this included a joint effort with Israel at their Dimona nuclear site.21 Israel already excelled at some aspects of cyber warfare, its efforts having begun as early as 1999, after an internal Israeli Red Team found massive vulnerabilities in its own networks. Israel launched a series of cyberattacks against Iran using malware. Iranian security officers caught one Iranian businessman, Ali Ashtari, whom they accused of trying to knowingly supply infected communications equipment at the behest of the Israelis. Ashtari was hanged at Evin Prison o
n November 17, 2008.

  Beginning in 2010, a series of unexplained computer viruses found their way into Iran’s nuclear facilities. The most significant was a carefully crafted bit of malware called Stuxnet. In June 2010, perhaps one-third of Iran’s functioning uranium centrifuges at the Natanz enrichment facilities broke, seriously setting back Iran’s program. The cause turned out to be a virus specifically designed to dramatically increase the speed of the centrifuges for short bursts while deceiving the safeguards into thinking they were still spinning at their regular speed. Security experts believed the evidence pointed to a joint U.S. and Israeli program, likely introduced into the Iranian computer system by an infected thumb drive brought into Iran’s Bushehr facility. Privately, Iranian officials suspected a Russian technician as the culprit for the contaminated virus. Neither the United States nor Israel acknowledged the attack, although in a video played at the 2011 retirement ceremony of Israel’s chief military officer, Lieutenant General Gabi Ashkenazi, the general claimed Stuxnet as an operational success on his watch as head of the Israeli armed forces.22

  Tehran accused both countries of mounting these computer attacks as part of a soft campaign to overthrow the regime. According to Iranian officials, the CIA also began a program to allow dissidents to maintain access to the Internet. Iranian intelligence minister Heydar Moslehi dubbed this an “internet in a suitcase,” apparently because it was a mobile system that amounted to a powerful router that when set up allowed the opposition to tap into the Internet, and even cell phone networks, while bypassing the security firewalls imposed by the Iranian government. An Iranian general said the design had been built in a fifth-floor office on L Street in Washington, financed by $2 million from the State Department, presumably from the funding approved by the Bush administration. To counter this soft-power attack, Iran formed its own cyber command, “equipped with state-of-the-art technology.”23

  If the U.S. government refused to engage in more lethal means, Israel and others were bound by no such restrictions. A series of bombings rocked Iranian oil pipelines and infrastructure. The terrorist group Jundallah stepped up its attacks on Iran. A string of bombings killed dozens of Revolutionary Guard officers, including a general, as well as numerous civilians. Iran, with some evidence, accused Israel of supporting the group. Starting on January 12, 2010, five attacks occurred against Iranian nuclear scientists in Tehran. Dr. Massoud Ali Mohammad, a fifty-year-old nuclear physicist who had backed the opposition candidates during the recent election, was killed when a remotely detonated bomb exploded as he left his home. Ten months later, prominent scientist Dr. Majid Shahriari and his wife were stuck in Tehran traffic on their morning commute. A motorcycle weaved its way between the cars and, with a faint click, attached a magnetic bomb to the driver’s side of the car. Seconds later it exploded, killing the doctor and wounding his wife. Twenty minutes later, a Revolutionary Guard scientist, Fereydoon Abbasi, was the victim of an identical attack. He managed to roll out the passenger side just in time to avoid the bulk of the blast. In July 2011, thirty-five-year-old academic Darioush Rezaeinejad was shot and killed by motorcycle-mounted assassins. Iran authorities later arrested one of the alleged assailants responsible for Ali Mohammad’s death, who prosecutors said had received training in Israel and agreed to carry out the attack for $120,000.24

  Not all explosions could be attributed to Israel. On November 12, 2011, Iranian Revolutionary Guard officers gathered at a rocket range twenty-five miles from Tehran for the test of a newly designed rocket motor for a planned multistage ballistic missile. Supervising the test was Major General Hassan Moghaddam, the Werner von Braun of Iran’s missile program. Iran’s military did not always adhere to the best safety practices; it had had more than ten serious accidents in just the past couple of years at this facility. Suddenly, a massive explosion rocked the Iranian base. In overhead images of the facility, it looked like a tornado had swept through it. The blast leveled nearby buildings. In the worst accident of the Iranian missile program’s history, Moghaddam died along with sixteen other officers and men.25

  Regardless of the cause, the sheer number of explosions created a mood of uncertainty and paranoia within the Iranian government. The pervasive sense that outside forces were behind every accident worked to the Americans’ and Israelis’ advantage. It created paranoia that played havoc with Iran’s nuclear and missile programs as scientists grew uncertain whether sabotage or design flaws set back their research.

  Iran tried striking back at Israel with less than professional tradecraft. In February 2012, it tried a string of attacks against Israeli diplomats in Georgia, Thailand, and India. Security officials uncovered all but one. Duplicating the attacks on them, a motorcyclist attached a magnetic bomb on the car of the wife of the Israeli defense attaché in India, seriously wounding her. Indian police soon arrested a fifty-year-old Iranian journalist as one of the culprits. In Thailand, one of the bombs went off prematurely in the safe house. As the Iranian agents fled, one bloody operative tried to flag down a taxi, who not surprisingly refused to accept the passenger. When police arrived, the same Iranian threw a grenade at them, only to have it bounce back off a tree and blow off both his legs.

  The CIA did not remain idle either. A number of presidential findings had been signed, going back to the Clinton years, to thwart Iran’s nuclear program. In 1994, the U.S. military had executed an operation called Project Sapphire, in which thirty-one nuclear specialists and three massive C-5 transport aircraft landed in Kazakhstan to secure 1,320 pounds of highly enriched uranium that had been improperly stored; intelligence had indicated that Iranian agents were interested in buying it.26

  In 2000, Langley hatched an idea to set back Iran’s nuclear program by having a former Soviet nuclear scientist, who had defected and now worked for the Americans, pass doctored blueprints for a TBA 480 high-voltage block—the triggering device needed to detonate a nuclear weapon. Embedded into the design was a sophisticated design flaw, one that would take the Iranians down the wrong path, ending not in a brilliant blast of a man-made sun, but a puff of smoke.27

  After briefing the Russian during a stay at a posh San Francisco hotel, the CIA turned him loose in Vienna. After stumbling around the city, he managed to find the Iranian delegation to the IAEA in an unmarked office in a five-story apartment building. After he dropped off the plans, American intelligence monitoring the building reported that a senior Iranian official suddenly changed plans and quickly returned to Tehran. Whether this Trojan horse operation proved effective remains unclear, but it seems likely it worked up to a point. At any rate, more than a decade later Iran still had not demonstrated any mastery of a triggering device.28

  The CIA received a windfall in June 2009. Shahram Amiri was a young nuclear physicist with a wife and children who worked with radioactive isotopes at Malek-Ashtar University of Technology in Tehran, which had close links to Iran’s nuclear program. How long he worked for the agency remains a matter of speculation—perhaps for several years, perhaps even providing input into the 2007 intelligence estimate on the Iranian nuclear program. For some reason, he came in from the cold or decided to defect while on a pilgrimage to Mecca. With the Saudis’ assistance, the CIA spirited him in complete secrecy to the United States for extensive debriefings about Iran’s covert nuclear weapons program. When he did not return, nervous Iranian authorities investigated, unsure of whether he had defected or been executed by Saudi Arabia or Israel. For his safety, the CIA secretly resettled him in Tucson, Arizona, well away from any Iranian communities.

  After a year in exile, Amiri grew homesick. Against the advice of his handlers, he called home to talk to his son. Iranian authorities answered the phone. Now they knew he had defected to the United States. Amiri was told to recant his defection or else his family would pay the price. To placate his family’s tormentors, he produced a video on his home computer saying he had been kidnapped and held against his will by the Americans. “During the eight months that I was kept in
America, I was subject to the most severe tortures and psychological pressures by the American intelligence investigation groups,” Amiri said. Iran released the video on state television.

  The agency tried to do damage control and protect Amiri’s family. It helped produce a slick video in which he recanted his story of abduction and reassured his family that he was safe in America, and released it on YouTube. “I am Iranian and I have not taken any steps against my homeland. I am not involved in weapons research and have no experience and knowledge in this field. I know that the government of the Islamic Republic of Iran will take care of and protect my family. I want them to know that I have never left them and have always loved them.”29

  Lonely and distraught, on July 13, 2010, Amiri showed up at the Iranian interests section at the Pakistani embassy near the vice president’s home at the Naval Observatory in Washington, D.C. He asked to be returned to Iran. Two days later, he arrived in Tehran, where after warmly embracing his seven-year-old son and his father, he held a press conference and claimed to have escaped from his CIA abductors, adding, “They offered me $50 million to cooperate with them and tell the media that I am a very important person in Iran’s nuclear program. They wanted me to show a laptop on the TV and say we have obtained very important information on Iran’s nuclear weapon program. But I promised myself not to tell [them] anything against my country.” The Iranian Fars News Agency claimed Amiri had been a double agent the entire time, working for Iranian intelligence—a possibility that the CIA considered too.30