On January 6, 1979, Bakhtiar announced the formation of a new cabinet, and the Shah announced that as soon as the parliament approved Bakhtiar’s government, he planned to leave Iran indefinitely. Khomeini denounced Bakhtiar’s government as illegal and in an act of defiance that reflected his confidence that victory was imminent, formed a shadow government, the Islamic Revolutionary Council, whose membership was largely kept secret in the early phases of the revolution. In 1980, 13 original members were identified. The Council was meant to carry out Khomeini’s will and oversee revolutionary affairs in anticipation of his return to Iran from exile. The Council also began laying the groundwork for a provisional Islamic government to take power that would serve as a transitional step in establishing an Islamic republic.

The formation of the Council was a seminal event in Khamenei’s career trajectory. Akbar Hashemi Rafsanjani, an ally of Khamenei since the early 1960s when they tried to orient the Qom seminary in a Khomeinist direction, was at this point one of Khomeini’s most trusted advisors. At Rafsanjani’s suggestion, Khomeini approved of Khamenei’s addition to the Council. By Khamenei’s admission, his ascension to the Islamic Revolutionary Council was a surprise, elevating him from a committed but peripheral revolutionary into Khomeini’s inner circle. Khamenei left Mashhad and headed to Tehran to serve on the Islamic Revolutionary Council in mid-January 1979. According to Khamenei’s official biography, the Council conducted backchannel negotiations with Pahlavi officials and contacted foreign diplomats, including Americans, to facilitate a transition. The Americans contacted the Council because the Carter administration did not see a feasible way to stop the Khomeinist opposition. So it hoped to preserve its Iranian interests by supporting more moderate elements and encouraging Khomeini to lessen his anti-American rhetoric.

Khomeini and his cohort, including several hundred fedayeen who had trained in Palestinian and Amal training camps in Lebanon during his exile, had planned several years of possible struggle, expecting elements of the armed forces to remain loyal to the government. To their surprise, on January 16, the Shah, who had secretly been battling lymphoma since 1973, left Iran for Egypt. Although he never officially abdicated the throne, he would never return to Iran. While Khomeini’s circle of advisors remained anxious that they would face resistance from Pahlavi holdovers, Khomeini decided that now was the time to return to Iran. The Islamic Revolutionary Council formed a welcoming committee, which Khamenei was a member of, to ensure and organize Khomeini’s repatriation.

Prime Minister Bakhtiar, who had been left in charge following the Shah’s desertion, agreed to let Khomeini return to the country in order to stave off potential unrest but warned him and his clerical backers that they must accept the central government’s authority even though they were aware of his plan to immediately establish a provisional Islamic government. Bakhtiar had a last-minute change of heart and offered to resign to delay Khomeini’s arrival. He also promised to hold a referendum within four months to allow Iranians to decide whether they preferred Khomeini’s Islamic republic or the continuation of the constitutional monarchy that was his favored path. Khomeini, who had all the leverage in the situation, refused to negotiate with Bakhtiar.

In a last-ditch gambit, Bakhtiar closed Iran’s airports, giving rise to allegations that he was trying to prevent Khomeini from returning on January 26, as he intended. Bakhtiar denied them, and claimed that the ayatollah “was free to come [to Iran].” Iranian radio said airport worker strikes had forced the closure. Still, this decision triggered protests and additional strikes throughout the country, including a large sit-in organized by Khamenei and other revolutionary clergy at Tehran University’s mosque. The pressure led to Bakhtiar’s capitulation, and on February 1, 1979, Khomeini returned to Tehran on an Air France 747, where he was greeted by several hundred international journalists and hundreds of thousands of ecstatic Iranians lining his procession route from the airport to Tehran’s city center.

While Bakhtiar was nominally still in charge, Khomeini was the true power broker from the moment he arrived in Iran. On the day of his arrival, Khomeini’s message was not one of unity but of vengeance against the Shah and the foreign powers who had propped him up and whom Khomeini believed might still be plotting to reinstall him, as happened during the 1953 coup against Mosaddegh. Upon landing at Tehran’s airport, Khomeini gave brief remarks in which he assailed foreign influence and vowed, “Our final victory will come when all foreigners are out of the country. I beg God to cut off the hands of all evil foreigners and all their helpers.” He then traveled 11 miles to a cemetery where many of the revolution’s victims were buried. There, he delivered a victory speech, proclaiming that Bakhtiar’s government was an illegal continuation of the Shah’s rule. Khomeini pledged not to negotiate and said that if Bakhtiar did not resign, he would install a provisional government and arrest Bakhtiar and other government officials. He further acknowledged a growing trend of defections from the ranks of the armed forces and called upon Iranian army generals to abide by the people’s will and join the side of the revolution.

Khamenei was among the revolutionaries at Tehran’s airport there to greet Khomeini. For the next ten days, he was a part of Khomeini’s entourage as the ayatollah set about consolidating power. During this period, Khamenei spearheaded a committee of the Islamic Revolutionary Council that promoted Khomeini’s various meetings, appearances, and decrees since returning to Iran.

On February 4, Khomeini announced that he was appointing Mehdi Bazargan as his prime minister and tasked him with forming a provisional government, preparing a referendum on the question of whether Iranians wanted to establish an Islamic republic, and creating a constituent assembly that would prepare a new constitution. The Islamic Revolutionary Council settled on Bazargan for the role as he was a figure who was palatable to Khomeini due to his religious orientation and who was useful due to his ability to comfort and shore up support from middle-class, intellectual, liberal, and nationalist constituencies for the revolution due to his commitments to gradualism, moderation, and democracy.

Bazargan reportedly negotiated behind the scenes on Khomeini’s behalf with SAVAK and the army chiefs for a peaceful succession, but on February 10, the order broke down. A group of young Islamist air force technicians staged a rebellion at a Tehran base, turning their weapons on their officers and fellow service members. This insurrection provided the impetus for Khomeini to enact his plan to distribute arms to loyalist mujahedin and fedayeen, as well as other armed groups, which his backers had stockpiled in mosques around the country, to use against the Shah’s armed forces. Over two days, numerous mullah-led guerilla units, leftist guerilla groups, and defectors from the armed forces attacked and successfully overran police stations, prisons, armories, and military bases around the country and seized palaces, ministries, and the national broadcasting apparatus. Several hundred were killed in the unrest. Finally, on February 11 at 2 p.m., the Shah’s Imperial Army declared its neutrality. Then, after it refused to quash the protests, the Shah’s prime minister, Shahpur Bakhtiar, resigned. The revolutionaries thereby claimed their final victory over the Shah; the broad-based Iranian Revolution was finally complete. Ali Khamenei recalled hearing an announcement come over the radio of the car he was traveling in, “This is the voice of the Islamic Republic of Iran,” and immediately getting out and falling to his knees in jubilant prayer.

The leadership role in the Iranian Revolution played by Khomeini and his clerical Islamist backers was the result of Khomeini’s ability to serve as a unifying figure for various interest groups – religious, secular, liberal-democratic, socialist, nationalist, Marxist, middle-class bazaaris, intellectuals, alienated urban working poor –  united only by their antipathy for the Shah and continued foreign interference in Iranian affairs. Iran’s disparate political factions bought into Khomeini’s heretofore vague vision of an Islamic Republic, as Khomeini hid his intention to install a theocracy predicated on velayat-e faqih and instead adopted disingenuous rhetoric, such as claiming he sought a democracy that would pursue political freedom and economic justice for the mustafadin (disinherited). Each faction brought its own competing and contradictory set of interests and expectations for the post-Shah era, but Khomeini was not interested in forging compromises or pluralistic governance. As soon as the Shah was toppled, he began the next phase of his plan, eliminating erstwhile secular and leftist allies to cement his theocracy.