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Special Features

Nuclear Confrontation, Khamenei’s Gift to Iran

September 19, 2020
Ehsan Mehrabi
17 min read
The nuclear confrontation, under Ayatollah Khamenei's command, has stunted Iran's political and economic development
The nuclear confrontation, under Ayatollah Khamenei's command, has stunted Iran's political and economic development
Foreign minister Javad Zarif insisted: “Those who are well-informed know we are not after a nuclear bomb"
Foreign minister Javad Zarif insisted: “Those who are well-informed know we are not after a nuclear bomb" is a review of Ayatollah Ali Khamenei’s 31-year record as the Supreme Leader of the Islamic Republic. The series focuses on one of the most secretive world leaders. Reports about his personal life are scant and, except for his son Mojtaba, whose name has been in the news only in recent years, the media has seldom published any reports or photographs of his family.

This mystery does not surround only his personal life and his family. Now, three decades after he ascended the throne as the most powerful individual in the Islamic Republic, short videos have come to light that reveal that his election as the Supreme Leader was meant to be a temporary measure. 

Business groups and institutions under the control of the Supreme Leader are one of the most secretive sectors of the Iranian economy: their financial dealings and profits and losses have never been transparent. Even in politics, the Supreme Leader refuses to act in a transparent way. He has shunned responsibility wherever he has been able to do so.

The series of reports tries to untangle the mystery of Khamenei.


Since the 1979 Islamic Revolution, the Islamic Republic of Iran has entered into two major and protracted confrontations with the West. The first was the eight-year Iran-Iraq from 1980 to 1988. during which, Iranian officials claim, the Islamic Republic stood up alone and all by itself against the East, the West and, of course, Saddam Hussein.

The second confrontation was not a military one, however. This skirmish between the Islamic Republic and the West broke out on the geopolitical stage just a few years after the war. It was the issue of Iran’s nuclear program, and the one to lead Iran into battle was none other than Ayatollah Ali Khamenei, the Supreme Leader.

This conflict entangled Iran in difficulties on every front. Economically Iran has suffered intensely from harsh, unparalleled sanctions. In its international relations Iran fell foul of Chapter 7 of the United Nations charter, which gives the Security Council the power to "determine the existence of any threat to the peace, breach of the peace, or act of aggression" and to take military and non-military action to "restore international peace and security". On the security side, the nuclear program became a prelude to turn Iran itself into a security threat both in the region and in the world. It also adversely affected Iran’s relations with many countries in the Middle East and beyond.

Since the Iran-Iraq war and almost throughout the tenure of three Iranian presidents, the nuclear program was the axis of Iranian foreign policy and cost the country enormously. It was at Ayatollah Khamenei’s behest that the conflict continued and, effectively, strangulated Iran’s political and economic development.


Failure to Justify Iran’s Nuclear Program

“Those who are well-informed know we are not after a nuclear bomb,” foreign minister Mohammad Javad Zarif, who was Iran’s UN ambassador from 2002 to 2007, says in a book-length interview with Mohammad Mehdi Raji, published in 2013 under the title Mr. Ambassador.

“But an analyst might ask: how come a country can accept sanctions in order to gain access to an energy source? The analyst then concludes that Iran has a security goal and wants to make a bomb. This is a general misunderstanding that has led people to view the question any way they want to.”

Zarif’s words lie at the heart of the confrontation between Iran and western powers: something Iran has never been able to justify or afford. The West never accepted that Iran, with its rich resources of oil and gas, was genuinely after peaceful nuclear energy. Even Ayatollah Khamenei’s fatwa proclaiming the development of nuclear weapons was prohibited by Islam could not convince the West.

Decisions about Iran’s nuclear activities were not made by any specific administration. The nuclear program was launched under the direct supervision of Ali Khamenei, continued under his direct supervision and still does. This decision was taken even though the companies that held nuclear cooperation agreements with Iran before the revolution were now refusing to work with the Islamic Republic, and Iran had not been able to force them to cooperate by appealing to international tribunals.

In fact, the decision by Ayatollah Khamenei pushed Iran into an arena that it knew nothing about – and in which it had no trusted international partner to ask for help. Consequently, the Islamic Republic’s nuclear activities were bound to be conducted underground.

Between 1997 and 2001 Iran began to secretly purchase equipment forits nuclear program, with the aim of enriching uranium domestically. But in 2002, the US disclosed evidence that Iran was trying to master the nuclear fuel cycle and had constructed installations to reach this goal. In response, the International Atomic Energy Agency (IAEA) stepped in and demanded the country explain itself.

Iran was forced to reveal some of its nuclear installations, such as those in Natanz and the heavy water reactor in Arak. As a result, in June 2003, Mohamed ElBaradei, the president of the IAEA, accused Iran of violating the Treaty on the Non-Proliferation of Nuclear Weapons (NPT). The body issued a strongly-worded resolution against Iran and demanded the country discontinue uranium enrichment.

In the meantime, Iran had been engaged in negotiations with France, Germany and the UK (E3), which led to what became known as Saadabad Proclamation. Iran promised to voluntarily suspend uranium enrichment and allow IAEA inspectors to inspect its nuclear installations, and in return, the E3 promised they would not take the matter to the UN Security Council.

Like the later Joint Comprehensive Plan of Action (JCPOA) negotiations that led to the 2015 nuclear agreement, the Saadabad negotiations were conducted under the direct supervision of Ayatollah Khamenei. In his memoirs, Rouhani writes that Khamenei directly asked him to “take a load off the back of the regime” by accepting the responsibility for the case.


In Direct Control of the Negotiations

During the Saadabad negotiations and between the meetings, as some negotiators said in a BBC documentary, Rouhani would consult the offices of President Mohammad Khatami and the Supreme Leader, asking them for instructions.

An informed source has said that when it was time to sign the joint statement, President Khatami and Hasan Rouhani paid Khamenei a visit and informed him that the discussions were over and the only thing that remained was to sign. Khamenei told them that they could sign it if they were confident that the dispute was over and that “they” – meaning the Europeans and the Americans – would not raise another issue after the statement was signed.

At a 2007 event with students of Yazd University, Khamenei recalled the nuclear talks that had taken place during the tenure of Mohammad Khatami. “In a meeting of responsible officials,” he said, “I said that if they wanted to drag this on I would personally enter the field, and I did so. I said, this trend of retreat must end, and it must change into a forward trend, and the first step must be taken by the administration that has been retreating. And this is what happened.”

At the time of the Saadabad negotiations, Iran believed that if its case went to the Security Council the US government and the five permanent members of the council would take control of events, leading to a resolution against Iran.  The IAEA’s board of governors had issued several resolutions against Iran prior to 2005 and Mahmoud Ahmadinejad’s presidency, but the case was never referred up to the Security Council. Even in the agency’s last resolution issued on November 29, 2004, the IAEA had emphasized “the  right  of  states  to  the  development  and  practical  application  of  atomic  energy  for  peaceful  purposes,  including  the  production  of  electric  power,  consistent  with  their Treaty obligations, with due consideration for the needs of the developing countries.”

In exchange for suspending uranium enrichment, Iran was supposed to receive concessions such as spare airplane parts and membership of the World Trade Organization. Not only were none of these promises kept, but the United States imposed further sanctions on Iran. The E3 had agreed Iran could keep some of its centrifuges and maintain the right to enrich uranium but, in the end, they failed to win Washington’s endorsement.

In his book The English Job: Understanding Iran and Why It Distrusts Britain, Jack Straw, the then-British foreign secretary, writes that when the E3 presented Saadabad to the Americans, the US wanted nothing to do with it. Knowing the accord was doomed without American approval, the E3 returned to Iran and tacitly told the Iranians that the “big boss” did not agree.

Iran had practically gained nothing from its agreement with the Europeans. But in the interim, it had succeeded in bringing a cascade of centrifuges online, so it decided to resume its nuclear activities. Contrary to general belief, the seals to the nuclear facilities were broken not during Ahmadinejad’s presidency but towards the end of Mohammad Khatami’s. In the book Mr. Ambassador, Zarif says he wrote an eight-page letter announcing the unsealing of nuclear installations – and of course, that Ayatollah Khamenei had encouraged him to do so.


Confrontation Instead of Negotiation

One the first acts of Mahmoud Ahmadinejad after he became president was to take advantage of the question of unsealing nuclear installations. Throughout his first four years in power, Ahmadinejad tried to present the Saadabad Proclamation as a humiliating attempt at compromise, and to paint himself as a rejuvenator pf Iran’s nuclear program. Principalists supported him unfalteringly in this propaganda drive. As a result, Iran’s negotiations with the West over its nuclear program became increasingly confrontational.

Disregarding the IAEA’s warnings, Iran continued to expand its nuclear program. As a result, its case was finally referred to the UN Security Council.

By 2008, the last year of George W. Bush’s presidency, Iran was operating more than 4,000 centrifuges and, according to American officials, had succeeded in producing more than half of the enriched uranium necessary to make one nuclear bomb. On the other hand, because of the reckless foreign policy of Ahmadinejad’s administration towards neighboring Arab countries, these countries put more pressure on Iran and were able to present Iran as a nuclear threat.

In a speech in the spring of 2009, Ahmadinejad called the Saadabad agreement “shameful”. “When, in Saadabad, they put together that one-sided, coercive and – I don’t want to say it, but – shameful agreement, they told themselves that the Iranian nation was finished,” he said. “They said all activities must cease, the labs must lock their doors, and courses on nuclear energy must be removed from the university curriculum.” He said these things despite the fact that the Saadabad negotiations were conducted on the orders of Ayatollah Khamenei and under his personal supervision. As usual, however, Khamenei did not pass any comment on Ahmadinejad’s statements.

Eventually, it was Rouhani who responded to him, after waiting a week. “Unfortunately,” he said, “these days most of the critical comments about the government’s nuclear diplomacy between 2003 and 2005 are wrong, biased and, in some cases, absolute lies.”

Once again, Ali Khamenei preferred to keep schtum – even though he had publicly supported the Saadabad Proclamation. Later, in an interview with Islamic Republic of Iran Broadcasting (IRIB) in 2013, Rouhani made Khamenei’s support for it public too. “Twelve days after [Saadabad] negotiations, the Leader said that these negotiations demolished the Israeli-American conspiracy,” he said. “If you want, I can read you the exact words by the Leader. This an example of the misrepresentation I was talking about. The IRIB repeated these misrepresentations so much that now you, yourselves, have come to believe it.”


Secret Negotiations with the US

Eventually, with increasing pressure on Iran during Ahmadinejad’s second term, Tehran decided to engage in negotiations in a more serious manner. George W. Bush’s administration needed a foreign policy win in his last few months in office, so agreed to send a representative to the ongoing negotiations between Iran and the so-called P5+1 group: the five permanent members of the security council, plus Germany.

And so it came to pass that in the summer of 2008, William Burns, the senior American negotiator, sat down for first time at the negotiating table with Saeed Jalili, Iran’s chief nuclear negotiator at the time. But according to Burns in his book The Back Channel: A Memoir of American Diplomacy and the Case for Its Renewal, this round of talks did not go well at all.

“Jalili then embarked on nearly forty minutes of meandering philosophizing about Iran’s culture and history, and the constructive role it could play in the region,” Burns writes. “Jalili wound up his comments by handing over an Iranian ‘non-paper’ [an unofficial diplomatic agreement].

“The English version was mistakenly headed ‘None-Paper’, which turned out to be an apt description of its substance. [EU foreign policy chief Javier] Solana and the rest of us looked at it quickly, at which point my French colleague helpfully groaned and muttered, ‘Bullshit’, which caused Jalili to look somewhat startled — and me to lose my game face.”

It seemed Ahmadinejad was unconcerned by the crisis that was coming Iran’s way. Instead, he used the nuclear program to sow divisions between the public and the Iranian political community. It was under Ahmadinejad that Iran’s nuclear program went beyond an international dispute and became a bone of contention among political factions inside Iran as well. And because of Ahmadinejad’s policies the Security Council passed a resolution against Iran, asking the Islamic Republic to stop enriching uranium.


Obama’s Carrot and Stick

When Barack Obama took over the presidency in 2009, official US policy towards Iran’s nuclear program changed. Obama promised to negotiate with Iran and, at the same time, strengthened the mechanisms for enforcing the sanctions.

In May 2009, Obama penned a lengthy, secret letter to Ayatollah Khamenei in which he emphasized that the US was determined to prevent Iran from building a nuclear weapon but, at the same time, he assured Khamenei that his administration was not after regime change in Iran and that he was willing to negotiate. As William Burns writes in his book, Khamenei’s response to Obama was “rambling, and at least by the standards of revolutionary Iranian rhetoric not especially edgy or sharp. President Obama responded quickly in a short letter that proposed a discreet bilateral channel for talks.”

In the meantime, sanctions against Iran remained in place. The disputed 2009 presidential election in Iran and its violent aftermath interrupted the progress towards negotiations. Following the election, Ayatollah Khamenei repeatedly criticized US policies towards Iran and, in one of his speeches, said that the US was covering its “iron fist” in a “velvet glove”: a reference to Obama’s offer to negotiate.

But then a new development changed the situation. A short while before the UN General Assembly convened in September 2009, American, British and French intelligence agencies discovered a secret nuclear site in the mountains of Qom, named Fordow, which could accommodate 3,000 centrifuges.

This piece of intelligence forced even China and Russia, which usually supported Iran, to put diplomatic pressure on the Islamic Republic. Eventually, on June 9, 2010, the Security Council adopted Resolution 1929 against the Islamic Republic and Iran was subjected to the most stringent international sanctions.

From here, it did not take long for Ayatollah Khamenei to take up the offer of secret negotiations with the United States. Aside from conducting secret negotiations in Oman in the last two years of Ahmadinejad’s presidency, he transferred for the nuclear case away from the Supreme National Security Council to the Iranian foreign ministry under Ali Akbar Salehi, thus diminishing the authority of Saeed Jalili as the chief nuclear negotiator.

The idea of secret negotiations with Iran had first been put forward by Sultan Qaboos, the king of Oman. According to William Burns, Sultan Qaboos informed Obama that he could contact Iranian officials who had permission from the Supreme Leader. While these talks were under way, Rouhani won the presidency in 2013 with the promise of resolving the nuclear issue and, with the green light from Ayatollah Khamenei, immediately entered into negotiations with the US.

This time around, Iran’s negotiators were Abbas Araghchi and Majid Takht-Ravanchi. From William Burns’ recollections we can conclude that these two were also acting under direct orders from Ayatollah Khamenei. According to Burns, “they were often guarded about the difficulties they faced at home, although they would sometimes confide that they had a Supreme Leader who was just waiting to say ‘I told you so’, and prove that the Americans could not be trusted, and that Obama was just as bent on regime change as Bush.”


“Heroic Flexibility”

Throughout the talks with Obama’s administration, Ayatollah Khamenei praised the efforts of the negotiating team. In a meeting with the commanders of the Revolutionary Guards in the summer of 2013, he famously described the nuclear negotiations as showing “heroic flexibility” and two months later, at a meeting with university students, he reiterated his support for them.

“Nobody should think these negotiators are compromisers,” he told them. “They are agents of the Islamic Republic. They are the children of the Revolution... We are not going to lose anything.”

But, at the same time, he let it be known that he was not optimistic about the outcome. In 2014, after the negotiations had been extended several times without a final agreement, Khamenei agreed that they should go on. “I am not against extending the negotiations, as I was not against negotiations in first place,” he said. “If these negotiations do not produce any results, the Americans will lose more, not us.” He also repeatedly emphasized that the West and especially the US could not be trusted and, personally, he was not optimistic about the outcome. “Of course,” he said in one speech, “as I have said before, I am not optimistic but...we firmly support our officials who are active on the diplomatic front.”

Even after the JCPOA was finally signed in Geneva, Ayatollah Khamenei responded very cautiously to the letter from Rouhani about the agreement – thus laying the groundwork to deny any responsibility for the agreement in future. In his letter, Rouhani had written that, with the Geneva agreement, Iran had been given the right to enrich uranium and its nuclear rights had been recognized by the US. But instead of explicitly acknowledging Rouhani’s “good news”, Khamenei tepidly thanked “the nuclear negotiating team and others involved.”

Some analysts believe that Khamenei adopted this tone because he wanted to both remain in charge of the negotiations and, at the same time, be able to deny responsibility for the results if it became necessary.

Besides, the sharp attacks on the negotiating team, both during the negotiations and after the JCPOA was signed, were mostly launched by entities within the Islamic Republic system that were directly or indirectly linked to the Supreme Leader. A number of Revolutionary Guards commanders, Friday imams appointed by Khamenei, and members of the Expediency Council and the Guardian Council constantly and harshly criticized both the negotiating team and the accord they had struck. Some of these attacks were led by Saeed Jalili, the former chief nuclear negotiator who, after Rouhani assumed the presidency, was appointed to the Strategic Council on Foreign Relations: a body that describes itself a “a think tank and advisory body to the Leader of the Islamic Revolution of Iran.”


No “Poisoned Chalice” for Him

Since his appointment as Supreme Leader Ali Khamenei has ceaselessly fought to maintain complete control over Iran’s nuclear program, while absolving himself of any responsibility for its consequences. The nuclear program used to be one of the most non-partisan issues in Iran’s foreign policy but became ground zero for warring political factions during the presidency of Mahmoud Ahmadinejad, and Ayatollah Khamenei never acknowledged this ideological split. Now that the JCPOA is foundering after Trump’s decision to unilaterally withdraw, Khamenei has chosen to blame the agreement itself. “Fortunately, even though the JCPOA did a lot of damage to us, the basics are still in place,” he once said, ambiguously. “Good things are being done and this is something the enemy does not want.”

Khamenei had asked Rouhani to “take a load off the shoulders of the regime”. But practically by himself, he has turned the nuclear issue into one of the heaviest burdens on the shoulders of the Islamic Republic. When Ayatollah Khomeini agreed to a truce with Iraq, he famously said that he was drinking from a poisoned chalice. But unlike him, Khamenei lacks the courage to so much as pick up the glass.


Also in the series: 

How Did Khamenei Become Supreme Leader?

Ruhollah Khomeini and Ali Khamenei: An Ayatollah and his Acolyte

The Overnight Ayatollah: Khamenei's Fight to Become a Spiritual Leader


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