Finally, in late 1998, a series of connected assassinations known as the “chain murders” took place quickly, exposing the intelligence ministry’s role in the decade-long serial killings. On September 15, 1998, Supreme Leader Khamenei called on the judiciary to rein in press outlets that abused freedom of the press. The following day, a special press court ordered the closure of a popular reformist daily newspaper and the arrest of its employees as “enemies of God.” A group of journalists concerned with the escalating hostility to the press moved to form a writers’ association. However, the leaders of the effort were summoned to the Tehran public prosecutor for interrogation in October 1998 and ordered to cease their activism. Over the next two months, five writers tied to the creation of the association were violently murdered.

President Khatami formed a committee to investigate the murders. Shortly thereafter, the committee blamed Saeed Emami, the deputy intelligence minister, when most of the killings occurred. Emami still served as an advisor to the hardline intelligence minister, Ghorban-Ali Dorri Najafabadi, who had been appointed at Khamenei’s insistence over Khatami’s objections during the “chain murders.” The committee alleged that Emami led a team of rogue intelligence agents who carried out the “chain murders” and most, if not all, of the roughly 80 suspicious deaths during the prior decade. According to the military prosecutor who tried his case, Emami had carried out several of the murders himself, including that of Ahmad Khomeini. Khomeini, who had engineered Khamenei’s rise along with Rafsanjani, ultimately became critical of the hardliners’ efforts to dominate Iranian politics and gave a speech denouncing them in early 1995. A month later, he died of an apparent heart attack. His death was alleged to have been caused by cyanide poisoning by Emami, who saw Khomeini as a liability to the Islamic Republic.

The exposure of the “chain murders” shocked and outraged the Iranian public, placing Khamenei and the hardliners on their heels. Khamenei denounced the attacks as “criminal, ugly, and hateful” and insisted that Iran’s enemies, particularly Israel, had a hand in the plot, working with corrupt actors in the intelligence ministry to paint the regime negatively. The intelligence ministry sought to walk a tightrope and put out an unprecedented statement in January 1999, acknowledging for the first time its participation in crimes but pinning the blame solely on Emami and his rogue agents. The ministry’s statement read, “The despicable and abhorrent recent murders in Tehran are a sign of a chronic conspiracy and a threat to the national security. Based on its legal obligations and following clear directives issued by the Supreme Leader and the president, the Intelligence Ministry set as a priority discovering and uprooting this sinister and threatening event. With the cooperation of the specially-appointed investigatory committee of the president, the ministry has succeeded in identifying the group responsible for the killings, has made arrests, and referred their cases to the judiciary. Unfortunately, a small number of irresponsible, misguided, headstrong and obstinate staff within the Ministry of Intelligence, who are no doubt under the influence of rogue undercover agents and acting towards the objectives of foreign and estranged sources when committing these criminal acts.”

The statement sought to shield the ministry’s senior officials from accountability by denying any knowledge of the murders, but even this effort at spin represented an admission of counterintelligence failure. Khatami demanded that Intelligence Minister Najafabadi resign or be fired, and in February 1999, Khatami replaced him with a reformist, temporarily wresting control back from hardliners of a key institution. The black eye suffered by the exposure of the targeted assassination campaign led Iran’s intelligence ministry to draw back from pursuing such prominent operations, but its general repression, harassment, and intimidation of dissent continued unabated.

In their investigative reporting, Akbar Ganji and Emad Baghi alleged that many prominent figures in the regime, in fact, had knowledge of and backed the “chain murders,” including former President Rafsanjani and his intelligence minister, Ali Fallahian. Gholam-Hossein Mohseni Ejei, who would later serve as intelligence minister during Mahmoud Ahmadinejad’s first presidential term and is currently the head of Iran’s judiciary, was also involved, according to Ganji. There was a great deal of speculation that the effort to pin the blame solely on Emami and rogue elements was a cover-up of higher officials' knowledge or direct involvement. This view was reinforced when Emami died suspiciously in prison, allegedly of suicide by ingesting hair-removal cream.

Amid the furor over the “chain murders,” the Islamic Republic held its first municipal council elections in February 1999. The reformists dominated around the country, indicating anger at the hardliners for their obstructionism and continued enthusiasm for Khatami’s reformism, even though his efforts at liberalization were backsliding. While it seemed the reformists were reaching a high-water mark, their project would soon unravel.

The regime went on to target the journalists who played a part in exposing the systematic campaign of assassinations. The judiciary gave Emad Baghi a three-year prison sentence for “propaganda against the Islamic Republic" and "divulging state secret information" and sentenced Akbar Ganji to six years in Evin prison. He alleged during his trial that during his pre-trial detention, he had suffered torture and abuse by guards, was placed in solitary confinement for three months, and was denied visitation by his family and lawyers.

Iranian authorities also banned three reformist newspapers – Salam, Khordad, and Sobh-e Emrooz – for their damning reporting on the decade-long string of regime-linked murders. In early July 1999, the majles approved a bill sharply limiting press freedom, and the subsequent closure of Salam on July 7, 1999, would trigger an unprecedented protest movement that began at Tehran University and soon spread around the country. On July 8, student groups at Tehran University held peaceful demonstrations against the new press law, the closure of Salam, and to air general dissatisfaction at the slow pace of reforms under Khatami.  Shortly after midnight, around 400 baton-wielding anti-riot police and plainclothes intelligence ministry operatives, most likely with ansar-e hezbollah vigilantes in the mix as well, stormed a student housing complex of Tehran University and began wantonly attacking students and destroying property. At least five students were killed, some reportedly thrown off balconies, and 200 were arrested.