International affairs, specifically as they related to the aftermath of the September 11 attacks and the launching of a U.S.-led “Global War on Terrorism,” was an additional factor undergirding the rise of the Iranian neoconservatives. The 9/11 attacks led to a brief pause in the enmity that had typically characterized the U.S.-Iranian relationship. President Khatami was among the first world leaders to condemn the attack, and Iranians held candlelight vigils and moments of silence at sporting events to honor the victims. On the Friday after the attacks, Supreme Leader Khamenei denounced the killing of civilians in a sermon broadcast to his followers in Iran and beyond. "Mass killings of human beings are catastrophic acts which are condemned wherever they may happen and whoever the perpetrators and the victims may be," said Khamenei.

Afghanistan, under the Sunni extremist Taliban, backed by Saudi Arabia and Pakistan, had emerged as the major proximate geopolitical threat to Iran after the Iran-Iraq War, and the first Gulf War had largely neutralized Saddam Hussein’s Iraq. The two countries nearly declared war in 1998 after the Taliban massacred Shi’a Hazaras and attacked an Iranian consulate while conquering Mazar-i-Sharif. Before the 9/11 attacks, Iran and the U.S. independently backed the Northern Alliance in their struggle against the Taliban. Immediately following the 9/11 attack, Khamenei called on the U.S. not to invade Afghanistan unilaterally, warning that establishing a U.S. military footprint in Pakistan and Afghanistan would multiply its regional problems. While Khamenei was happy to eliminate the Taliban, he assessed that a long-term U.S. presence in its backyard would be a greater headache for Iran. Still, Iran’s leadership backed a multi-lateral approach, preferably under U.N. auspices, to confronting the Taliban and even offered to participate in such a coalition.

Once the U.S. decided to lead its invasion, Khamenei opted to take advantage of the opportunity. Khamenei empowered IRGC-Quds Force Commander Qassem Soleimani, who would soon become Khamenei’s primary agent for confronting the U.S. and Israel and expanding Iranian influence around the region, to conduct several rounds of covert shuttle diplomacy with U.S. diplomats. Iran went so far as to share intelligence with its U.S. counterparts during this time, hastening the fall of the Taliban government. Iran then played a productive role in the negotiations to stabilize Afghanistan, giving critical backing to the U.S. efforts to install Hamid Karzai. Iran’s efforts were not merely philanthropic; once the U.S. decided to invade, Khamenei and Soleimani oriented their efforts to ensure that Afghanistan would remain weak but stable, funneling arms to insurgents of various stripes so that it could build influence with all players (including the Taliban) and attack the U.S. military by proxy.

One of the Iranian interlocutors in the secret U.S.-Iranian negotiations revealed to the head of the U.S. delegation that Soleimani, pleased with the cooperation, had been considering, at great political risk as he was not yet the revered figure he would later become, a reevaluation of Iran’s ties with the U.S. More conservative figures within Iran, including Supreme Leader Khamenei, were cautiously on board with the idea of partnering with the U.S. toward the limited tactical end of confronting the Taliban but remained skeptical of U.S. motives. However, it is unclear to this day how accurate the Iranian interlocutor’s description of Tehran’s readiness to work with Washington was. In January 2002, the U.S. signaled its skepticism of Iran when President George W. Bush labeled Iran part of an “axis of evil” in his State of the Union address. With characteristic bluster, Khamenei responded that U.S. foreign policy was the world’s “greatest evil” and that denunciation by “the most cursed of the world’s satans” was effectively a badge of honor.

The subsequent U.S. invasion of Iraq in 2003 confirmed Khamenei’s perception of the U.S. as bent on Iranian regime change like never before. The U.S. was no longer the distant “Great Satan” but a proximate threat with an expanding military footprint in the region that had toppled two neighboring governments. The initial success of its invasion of Iraq caused Khamenei great alarm, especially given that the U.S. justified its invasion on the need to preempt Iraq from obtaining weapons of mass destruction. In August 2002, the National Council for Resistance in Iran (NCRI), the diplomatic arm of the MEK, had exposed that Iran was building undisclosed uranium enrichment and plutonium reprocessing facilities at Natanz and Arak in violation of its obligations under the Nuclear Non-Proliferation Treaty. While Khatami and Khamenei insisted that Iran would never seek a nuclear weapon and that Iran’s right to peaceful nuclear energy was sacrosanct, they became desperate for a resolution to the nuclear impasse lest the U.S. turned its sights on Iran next.

In May 2003, Khamenei secretly approved a proposal by Khatami to offer the U.S. negotiations on a “grand bargain” that would resolve all outstanding issues between the two countries, including its nuclear program and support for terrorist groups such as Hezbollah and Hamas. Iran sent its offer to the U.S. through a back channel, using the Swiss ambassador to Iran to convey Iran’s willingness to negotiate. U.S. officials rejected and later downplayed the significance of the Iranian proposal.

The Iranian system was left with a difficult choice: Yielding on its nuclear program would be seized upon as a betrayal of Iran’s sovereignty by its domestic enemies while pressing ahead defiantly would bring isolation from Europe and potential confrontation with the U.S. After the failure of the “grand bargain” offer and in the face of mounting international pressure over its nuclear program, Khatami entered into negotiations with the IAEA and E3 (the UK, France, and Germany). Iran agreed during the negotiations to suspend its enrichment activities, allow snap IAEA inspections, and adopt an additional protocol to the NPT that would restrict its nuclear program. While Khatami could not have made these concessions without Khamenei’s blessing, Khamenei was happy to allow Khatami to absorb the opprobrium of hardline clerics and IRGC officials, who accused Khatami of selling out Iran, undermining its deterrence, and advancing U.S. interests.

The February 2004 majles election demonstrated that the marginalization of the reformists that first became apparent during the prior year’s municipal elections was now complete. The Guardian Council nearly touched off a crisis the month before the election, disqualifying almost 2,500 reformist candidates in its most nakedly political show of power yet, but the reformists were feckless and divided over how to respond. The reformists went from dominating the majles to controlling just 16 percent of seats, while the conservative coalition won 67 percent. A neoconservative from the Abadgaran faction was appointed Speaker, reflecting the far-right’s rise to dominance within the conservative coalition.

By the end of the Khatami administration, Supreme Leader Khamenei had succeeded in quelling the reformist current, using the structural advantages of his position to not cede ground to the presidency. Ever the skillful politician, he grew societal demands for greater freedoms by giving ground where necessary. He also used the institutions loyal to him – the judiciary, the IRGC and security services, and the Guardian Council – to suppress any meaningful change. His skill was most evident in how he discredited Khatami and the reformist political elite in the eyes of the public, drawing them into his toxic embrace when calls for change threatened regime stability. He also allowed Khatami leeway to negotiate and compromise with the West when the war on terrorism and the international focus on Iran’s nuclear program threatened Iran’s position. At the same time, he undermined these efforts and ensured that accountability for failure would land solely on Khatami and the reformists. The failures of the Khatami administration ushered in a sea change in the Iranian body politic, as reformists increasingly grew disaffected and the urban poor and working classes shifted their allegiances to the resurgent conservative movement, which used populist rhetoric to give the appearance that it would address their economic plight.