Ayatollah Khomeini died on June 3, 1989. Khomeini’s health had been an issue since he assumed the Supreme Leadership and became more concerned after he suffered a heart attack in 1986. Throughout his final years, finding a suitable successor who could carry on his radicalism legacy and ensure the revolutionary regime's continued survival was one of his primary preoccupations. Khomeini’s unique charisma and religious stature enabled him to amass nearly absolute power and to prevent the bitter ideological factionalism among the clergy from derailing the ship of state. He was adept at maintaining the precarious balance between the Islamic Left and conservatives, preferring to stay out of most of the day-to-day squabbling. He did not heavily favor one side over the other when compelled to intervene. His pronouncements carried such weight that the losing party would have no choice but to follow his dictates, never losing esteem for the Imam.

Iran had undergone a systemic transition in 1979 from a monarchy to the Islamic Republic. However, the question that loomed large was whether the revolutionary regime, which emerged weakened following a bloody decade spent contending with an internal insurgency and a brutal external war, could survive a leadership transition following the passing of its founder and central figure. There were forces both within and outside the country that saw the death of Khomeini as an opportunity to exploit Iran’s weaknesses and divisions and potentially topple the Islamic Republic. Khamenei weighed in at the time, saying, “The enemy already had sinister plans for the period following the Imam’s illness and death. Financial Times reported that with the leader's death, there would be a huge gap in the political system of Iran – a gap that would be impossible to fill. Radio America reported that Imam’s death would be followed by instability throughout the country and this might even ignite civil war in Iran.”

In authoritarian systems, leadership transitions are typically accompanied by uncertainty, if not outright crisis. Even in systems with clear-cut procedures for succession, newly installed leaders must gain the support, or sufficient fear, of a broad swath of the general population to establish stability and stave off a popular uprising. At the elite level, they must gain buy-in from key security and political heavyweights and balance competing factions and personalities wrangling for power, influence, and patronage. They very quickly need to cultivate allies and core constituencies that can help them survive and either coopt or marginalize potential adversaries, often through heavy-handedness and repression. They must often resort to arbitrary enforcement and frequent, sometimes capricious changes of rules and norms to maintain their grip on power.

President Ali Khamenei was ultimately picked as the successor to Ayatollah Khomeini. As a mid-ranking cleric who lacked the religious legitimacy and charisma of his predecessor and was overshadowed by several of his political rivals, Khamenei was a surprising choice nobody expected could fill the Imam’s shoes. His political survival and that of the Islamic Republic were far from assured. Yet, he displayed a surprising political acumen that enabled him to retain power and play a more hands-on and consequential role than even Ayatollah Khomeini for over three decades. While his reign has brought immiseration and increased repression to Iran and sectarian conflict and instability throughout the Middle East, Khamenei and the Islamic Republic have endured.