Khamenei criticized the assailants for their excesses and called for justice to be served, but his words rang hollow as he had fanned the flames of press hostility and vigilantism since the reformists began their ascent. News of the dorm room attack catalyzed five days of student-led anti-conservative, anti-Khamenei protests, spreading to 18 Iranian cities. By daring to openly criticize Khamenei and provocative chants of “Khamenei must go!”, the protestors were touching the third rail of Iranian politics, challenging the legitimacy of the concept of velayat-e faqih, the regime, and the Islamic Revolution itself.

Each reformist demonstration was met with counter-demonstrations by student basijis, ansar-e hezbollahis, and other pro-hardline forces, and both sides became increasingly radicalized as tensions flared, with the conservatives accusing the reformists of undermining Islam and the velayat-e faqih regime. The IRGC viewed the situation as a threat to the foundations of the Islamic Republic and leaned on President Khatami to rein in the demonstrators, using thinly veiled threats against not just the protestors but Khatami himself. In a letter signed by 24 IRGC and basij commanders several days into the protests, they cautioned Khatami that they would be forced to act if he would not, saying, “How long should we observe the situation with tears in our eyes? How long should we suffer in silence and practice democracy through creating chaos and insulting each other? How long should we practice revolutionary patience while the system is being destroyed? Mr. President: If you do not make a revolutionary decision and if you do not fulfill your Islamic and national mission today, tomorrow will be far too late. It is unimaginable how irretrievable the situation will become. In the end, we would like to express our utmost respect for your Excellency and to declare that our patience has run out. We cannot tolerate this situation any longer if it is not dealt with.”

The IRGC commanders’ letter was notable for showcasing their disdain for democracy and the republican elements of the Islamic Republic. This was the first major intervention into domestic politics by the IRGC, which had grown increasingly rich and powerful as an institution outside of the limelight. In effect, they were putting Khatami on notice that if he did not move to restore order, it would imperil not only his political fortunes but also the institution of the presidency itself.

Khatami, who was at his core loyal to the principles of the Islamic Revolution, heeded the IRGC’s warning and, whether out of duress or genuine conviction, denounced the protestors’ anti-regime slogans as “demagogic, provocative, and a danger for the national security.” Khatami’s denunciation of the student uprising tainted him as a regime apparatchik in many reformists' eyes. It served as a wake-up call to the more idealistic-minded that politicians dependent on good standing with Khamenei and the regime could not be trusted as vessels for overhauling Iran’s revolutionary system, which was the genesis of the nation’s ills.

Despite Khatami’s call for restraint and a government ban on further protests, the protestors returned to the street, where they were violently confronted by law enforcement, the intelligence ministry, anti-riot special units, and thousands of ansar-e hezbollah vigilantes. The regime also mobilized tens of thousands of supporters – many who were reportedly government workers given the day off and bussed to Tehran – for a countervailing demonstration and show of force. The counter-protestors took back the streets, and many pro-reformist demonstrators who showed up were beaten and/or detained. Although pacified, the 1999 student demonstrations marked the beginning of a sustained protest movement against the regime, which has cropped up repeatedly over the years in response to its worst excesses.

The tumult, which was unlike anything Iran had experienced since the revolution, shook both Khamenei and Khatami’s confidence in their positions. For a period, the two improved their working relationship. Khamenei demonstrated his penchant for pragmatism when it served him or when he was pressured and gave amnesty to most arrested protestors. The regime tried and sentenced many of the perpetrators of the dorm room attack that precipitated the protests to demonstrate that the rule of law still applied. Khamenei replaced the hardline head of the judiciary, Ayatollah Yazdi, with a more pragmatic conservative. These measures were part of a push-and-pull dynamic wherein Khamenei would allow some liberalizing reforms to be enacted. However, then his hardline allies in and out of government would act to undermine Khatami’s agenda.