The ailing Ayatollah Khomeini was embittered by the war's end and was loath to see his revolutionary ardor give way to a spirit of pragmatism. The end of the war removed the pretext of a national security emergency. Critics, including many clerics who had been Khomeini loyalists, felt as though they could now criticize Khomeini’s exercising of near absolute power and the lack of a clear political, economic, and military strategy for prosecuting the war, without fear of being accused of aiding the enemy or being counterrevolutionary. Khomeini did not wish for the Islamic Republic to evolve in a less religious, less ideologically driven, and less confrontational direction and spent his final months ensuring that his legacy of radicalism would continue after his passing.

His first order of business was a purge of political prisoners within Iran’s prison system, a massive bloodletting and human rights atrocity that tested his disciples' devotion. Leaked recordings would later reveal that the regime had considered mass killings of political prisoners for several years, but the pretext that finally greenlit the plan came in the days immediately after Iran accepted U.N. Resolution 598. During the war's later years, after its expulsion from France, the MEK remnants in exile had established a military headquarters in Iraq from which they planned to eventually topple the Islamic Revolution and had fought alongside Iraqi troops in some of the combat in Iraqi Kurdistan. Iran’s accession to the ceasefire signaled to the MEK that the regime was weak, and the MEK launched an ill-fated invasion across Iran’s western border. The MEK combatants penetrated 90 miles into Iranian territory, further than Iraq had during the conflict. They occupied a few cities and towns, declaring their intention to advance to Tehran and topple the regime. The IRGC reversed the incursion in a matter of days. MEK members who could not retreat were killed in combat or executed on the spot.

Khomeini used the MEK invasion to claim an extant wide-ranging conspiracy for a MEK-led uprising and issued a secret fatwa ordering the execution of any prisoners who retained loyalty to the MEK. Khomeini’s fatwa established death commissions in each province comprised of judicial, prosecutorial, intelligence, and prison officials who held summary trials outside any established legal or legislative framework and, following arbitrary questioning, put an estimated 5,000 prisoners to death. Amnesty International said the executed were mostly accused MEK affiliates but also secular leftists. The campaign reasserted revolutionary terror in Iran and pacified hardliners around Khomeini who feared that an atmosphere of relaxed social liberties and free expression after the war would lead to moral degradation and the dampening of revolutionary fervor. President Khamenei was one such leader who backed Khomeini’s brutality in the 1988 prison purge. In December 1988, he was quoted in an official newspaper as saying, “Do you think we should hand out sweets to a person who has been involved from inside prison with the activities of monafeqin (hypocrites) who launched an armed attack within the borders of the Islamic Republic? If his relationship with that apparatus has been made clear, what should we do to him? He is punishable by the death penalty and we would certainly execute him.” Khamenei’s willingness to go along with the regime's worst excesses would contribute to his succession as Supreme Leader months later.

Ayatollah Khomeini’s last major public act as Supreme Leader was also calibrated to ensure that Iran would take the path of revolution over pragmatism and reconstruction after his death. On February 14, 1989, just four months before his death, Khomeini issued his infamous fatwa placing a religious duty on Muslims worldwide to kill British author Salman Rushdie over what he labeled blasphemous passages in his book, The Satanic Verses. The Rushdie affair was a seminal chapter in Iran’s efforts to export the Islamic Revolution and heralded Iranian-inspired Islamism’s arrival as a security threat to the West. According to Khomeini biographer Baqer Moin, “By issuing the fatwa, Khomeini had made a serious bid for the leadership of the entire Islamic world, while, at the same time, finding a way to refocus the energies of those of his supporters at home who had been demoralized by the long, bloody inconclusive war. From being regarded by most non-Shi’a as merely a renewer of Islam, through the fatwa he became a spokesman for the frustrations and ambitions of Muslims in general, and not just those in Islamic countries. Compromise with the society around them was becoming a less and less attractive option among militant Muslims in Europe, and in the art of refusing to compromise there was no mentor more reliable than Khomeini.” 

With his final two major acts before his death, the 1988 prisoner massacre and the Rushdie fatwa, Khomeini signaled that Iran should continue to be more repressive and confrontational toward the West in its foreign policy after his departure from the scene. An internal struggle lasting decades would ensue over whether to take a more pragmatic or stridently revolutionary path, but the forces advocating the hardline approach have typically retained the upper hand, even when popular sentiment has forced brief experiments with domestic reforms and conciliation on the international stage. The story of Khomeini’s successor, Ali Khamenei, has been one in which the Islamic Republic emerged from a weakened state following the Iran-Iraq War to become one of the leading threats to regional and international security, as well as a serial abuser of human rights of its citizenry.