Following the passage of Iran’s constitutional referendum in December 1979, the country turned its attention to its first-ever presidential and majles elections in early 1980. Khomeini was wary of the potential backlash among secular and moderate Iranians if the proceedings gave off the appearance of an imposition of clerical rule over Iran’s nascent republican institutions. In the interest of legitimizing the Islamic Republic’s new hybrid system among the population writ large, not just his followers, Khomeini barred clerics from running for the presidency. Numerous other candidates were also disqualified, including Mas’ud Rajavi, the leader of the Mojahedin-e Khalq (MEK). This Islamist Marxist movement was part of the coalition to oust the Shah. However, Khomeini sidelined it after the revolution due to its rejection of velayat-e faqih and the decision to boycott the December 1979 referendum.  

The IRP’s lay candidate had to withdraw when it came out that his father was Afghan, contradicting the new Constitution’s demand that the President be of Iranian origin and nationality. He was replaced by an obscure candidate who came in a distant third, garnering just over 3 percent of the vote. Despite the IRP’s paltry showing, the election did not indicate that the Khomeinists lacked favor with the population, nor was it a sign of organizational weakness. The winning candidate, Abolhassan Banisadr, who amassed more than 75 percent of the vote, was popular with the left but was also closely associated with Khomeini in the public’s mind due to his role as an advisor during Khomeini’s exile in Paris. Banisadr favored an Islamic government for Iran, although his vision was more democratic than Khomeini’s. He saw Khomeini in the pre-revolutionary period as a useful vessel to gin up anti-Shah and anti-foreign domination sentiment. He helped make Khomeini a palatable figure among Iran’s intelligentsia. Thus, Khomeini saw Banisadr as a figure he could work with until he was no longer useful.  

Banisadr was inaugurated as a powerful figure on February 4, 1980, serving as President and head of the armed forces and Supreme Defense Council after Ayatollah Khomeini transferred his constitutional authority as commander-in-chief to Banisadr. Reflecting Khomeini’s support, Khamenei, in his capacity as Tehran Friday prayer leader, exhorted his followers to “respect him, follow him, support him in the field, cooperate with him, do not undermine him.” The goodwill would not last, however, as Banisadr saw in his victory a mandate to chart a more moderate course for the revolution and to rein in clerical power. In his words, he sought to rescue the revolution from “a fistful of fascist clerics.” He abortively sought to pursue an agenda that included integrating the IRGC into the regular army, dissolving revolutionary courts and reestablishing a centralized justice system, and doing away with the excesses of property expropriation to create a stable economic development and investment environment.

The IRP, led by its powerful secretary-general, Ayatollah Beheshti, offered Banisadr limited support at the beginning of his presidency, conditioned on following the Khomeinists’ preferred path of militant Islamism. Ayatollah Khomeini also appointed Beheshti as chief justice of the supreme court, and his control over the IRP and judiciary gave him considerable influence over the Khomeinists’ primary instruments of revolutionary terror. Beheshti’s appointment as chief justice further ensured that Iran’s legal system would be immune to secularist or liberal reformation efforts and instead take an Islamist trajectory. Banisadr’s agenda, which called for a “year of order and security,” was essentially predicated on reining the Khomeinists’ excesses. So he was frustrated at every turn by the IRP, which was loath to integrate its parallel network of institutions, such as the IRGC and revolutionary tribunals, into a unified central government.

The limitations on Banisadr’s power became apparent early on due to the growing ascendance of the IRP, which won an outright majority of seats in the majles elections held in March 1980. Unlike the presidential election, Khomeini explicitly encouraged clerics to run for the majles and called on the population to “vote for only good Muslims.” In addition to placing his thumb on the scales in this manner, Khomeinist thugs in the komitehs attacked rallies and offices of rival parties, most notably the Mojahedin-e Khalq, which failed to win a single seat despite its growing popularity.

Following its resounding victory in an election marred by allegations of intimidation and irregularities at the polls, the Khomeinist majority selected Akbar Hashemi Rafsanjani as Speaker of the Parliament. Ali Khamenei had resigned as head of the IRGC to run in the majles elections, and he won a seat as a representative from Tehran. Reflecting his good standing with the party, Khamenei served as the head of the defense committee, where he prioritized bolstering the IRGC’s armed strength and integrating the Basij, irregular paramilitary volunteer units, into the IRGC.

Over the next few months, bitter wrangling ensued as the IRP moved to block several of Banisadr’s allies from serving in his cabinet, as well as his preferred choices for prime minister, leaving him no choice but to select an IRP candidate, Mohammad Ali Rajai. Banisadr had hoped that his ability to handpick a prime minister would enable him to appoint an ally who would be a rubber stamp for his agenda, ensuring that the presidency would evolve as a stronger office than the prime minister. He failed to predict the IRP’s dominance at the polls, which stripped him of that ability. As a result, the prime minister became a more powerful position until the role was eventually abolished. Banisadr frequently clashed with Rajai, whom he viewed as an incompetent ideologue. However, Rajai had the upper hand due to the backing of Beheshti and the IRP, although Khomeini himself tried to stay above the political fray.

Months into his presidency, the IRP controlled the parliament, the judiciary, and the president’s cabinet, ensuring that Banisadr could not govern effectively. The ascendant IRP moved to purge modernists and technocrats from government ministries, replacing them with revolutionaries acceptable to the emerging Khomeinist order. The Islamic Revolutionary Council formally launched a cultural revolution during this period, which also sought to transform Iran into a conservative Islamic society through repression, purging any vestiges of Western, liberal culture and values. Iran’s universities were the primary battleground, as they were the focal point for leftist and liberal education and political organizing.

Ayatollah Khomeini set the stage for an attack on Iran’s universities in April 1980, declaring, “We are not afraid of economic sanctions or military intervention. What we are afraid of is Western universities and the training our youth in the interests of West or East.” Shortly after that, Khomeinist komitehs violently clashed with leftists, forcing them out of universities. Professors, many of whom had actively opposed the Shah, were now deemed insufficiently revolutionary and were dismissed. Ultimately, Iran’s universities were shut down for three years while the newly formed High Council on the Cultural Revolution moved to Islamize the curriculum of Iran’s entire education system.

The Khomeinists also moved to pressure women from participation in public life and imposed repressive mores against them. The number of political prisoners ballooned during this period to pre-revolutionary levels, and executions of political prisoners and those accused of morality crimes increased.  Many professors, students, doctors, and engineers fled Iran, creating a dearth of expertise that has plagued the country today. The Iranian system was effectively recalibrated to prioritize devotion to Islam and the revolution over technocratic expertise.

In September 1980, the Iran-Iraq War threatened to topple Iran’s post-revolutionary government but instead actually accelerated the Khomeinists’ consolidation of power. Saddam Hussein, the Sunni leader of a majority Shi’a nation, was wary of the Islamic Revolution next door, which had energized Iraq’s oppressed Shi’a population, and of the Khomeinists’ explicit desire to export the revolution. Khomeini hated Hussein ever since being banished from Najaf and frequently demonized the secularist leader publicly as an infidel. Unsatisfied with a 1975 treaty inked with the Shah to resolve a border dispute over the Shatt al-Arab River, Hussein saw an opportunity to redraw the map in his favor and blunt the momentum of the Islamic Revolution in its infancy.

Sensing the Islamic Revolutionary regime was weak and vulnerable due to the domestic political turmoil and ethnic unrest gripping the country and its international isolation as a result of the still-ongoing hostage crisis, Hussein launched a surprise invasion on September 22, 1980, seeking to seize the oil-rich province of Khuzestan, which also contained numerous strategic waterways and coastal access to the Persian Gulf. The Iranian armed forces were in disarray on the eve of the Iran-Iraq War due to ongoing purges of its officer class and the inability to procure needed weaponry and parts from the West. Iran’s defenses along the Iraqi border were weak, as much of the military’s existing capacity was tied up in pacifying ethnic conflicts in restive provinces.

Hussein thought the Arab population of Khuzestan, which had been agitating for local administrative and cultural autonomy, would welcome his incursion and rise on behalf of Iraq. However, instead, the war united Iranians under the banner of nationalism. The Khomeinists sought to imbue the fighting with Shi’a symbolism and appeals to martyrdom, which inspired huge numbers, particularly of the basij, to give their lives in “human wave” assaults to repel the Iraqi invasion. Iranians of all backgrounds rallied to the flag and joined in the cause of the “Sacred Defense” of their homeland. The Iran-Iraq War further hardened enmity toward the U.S. as well, as Khomeini and his followers viewed the conflict as an imposed war on behalf of American and Western interests to topple the Islamic Revolution and gain back control over Iranian energy resources and strategic waterways. The U.S. did not encourage Saddam Hussein to invade Iran, nor did it actively arm him until Iran had gained the upper hand in the conflict. In their conspiratorial worldview, the U.S. and its allies opposed a revolutionary, independent Iran that would not uphold their interests in the region and would go to great lengths to sabotage the revolutionary regime and return Iran to a vassal state. Saddam Hussein’s brutality in waging war, including using chemical weapons and carrying out aerial bombings of civilian population centers, had long-lasting psychological scars and are used to the present day as evidence of U.S. perfidy and to justify claims that the U.S. existentially threatens the Islamic Revolution.

Ali Khamenei was active in the war effort from the outset, participating in military planning meetings on responding to the Iraqi invasion. Days into the conflict, he volunteered to go to the front lines to prepare a report on the condition of Iranian forces and their needs. He would spend the first few months of the war, from September 1980 until June 1981, going back and forth between the front lines. He was not on active duty but did assist combatants and participate in some operations while continuing to perform his duties as Friday prayer leader. During this period, Khamenei also served as Khomeini’s representative on the Supreme Defense Council, an umbrella body created in October 1980 to serve as a unified command for Iran’s conventional armed forces and the IRGC. Khomeini appointed Banisadr as the chairman of the Supreme Defense Council. This position gave him the trappings of authority and made him a convenient scapegoat set up to fail.

Despite the efforts to align the activities of Iran’s conventional and irregular forces, tensions remained, and the Khomeinists’ mistrust of the conventional military continued unabated. These tensions would contribute to the undoing of President Banisadr, who backed the conventional armed forces over the IRGC. The Khomeinists suspected Banisadr would use his ties to the conventional forces to launch a coup. They leveraged these fears to secure better equipment for the IRGC, allowing it to strengthen its position relative to the conventional forces. According to a study of the Iran-Iraq war by the Center for Strategic and International Studies, “The situation was made worse because the regular forces tended to husband their resources while trying to organize for counteroffensives, while the Pasdaran (IRGC) infantry was constantly at the front of the day-to-day fighting and took most of the casualties.  The Pasdaran got virtually all the favorable coverage in the Iranian media, while the Mullahs began to accuse the regular forces of sacrificing the Pasdaran while protecting their own lives. The net result was that President Banisadr increasingly came to rely on his role as commander-in-chief of the regular forces as a basis for power under conditions which cost him both religious and popular support.” During this period, the IRGC expanded through recruitment, as it came to be mythologized as the true guarantor of the revolution. It also became a more sophisticated, professionalized, and better armed fighting force with invaluable combat experience.