The first wave toppled Shah Mohammad Reza Pahlavi in January 1979. The second consolidated power in the hands of Khomeini and his supporters at the expense of many other groups, including secular ones, that had made common cause with his camp.
The consolidation-of-power phase of the revolution saw the Islamic regime employing its security services against rivals in exile.
Outside Iran, perhaps the best-known case was that of Shapour Bakhtiar, the last prime minister of the shah's era and a prominent opponent of the Islamic Republic. He was stabbed and killed in his Paris home in 1991. A French investigation led to the imprisonment of several individuals who were believed to have been intelligence agents of the Islamic Republic.
In 1992, an attack on Kurdish opposition leaders in a Berlin restaurant, the Mykonos, caused such an uproar that it led to a major breakdown in attempts to improve ties between Iran and the European Union.
Mehdi Ebrahimzadeh was among nine people hit by automatic-weapon fire in the Mykonos. He recalled the trial that followed the incident:
"On 17 September 1992, the restaurant was drenched in blood with the commando-style terrorist attack of the agents of the Islamic Republic, in which four opposition figures were killed. With four to five years of judiciary investigations and hearings that followed, the outcome was the trial of top officials of the Islamic Republic. In April 1997, for the first time a European court issued a sentence, in which it named Supreme Leader Ali Khamenei, President Hashemi Rafsanjani, Foreign Minister Ali Velayati and most important of all, Intelligence Minister Ali Fallahian, as the person who implemented the collective decision of physically eliminating the opposition -- in this case, the leaders of Democratic Party of Kurdistan. The verdict also mentioned other assassinations, including the assassination of Dr. Qassemlu in Vienna and Dr. Shapour Bakhtiar in Paris," Ebrahimzadeh said.
Following the German court's verdict, Iranian officials denied having any role in the Mykonos killings. However, European Union countries recalled their ambassadors from Tehran to emphasize that Europe would not tolerate Iranian state sponsorship of terrorism. The ambassadors returned again in late 1997 after the EU became convinced that Iran's Intelligence Ministry -- at least in future -- would not carry out political assassinations on European soil.
Inside Iran, thousands have perished in apparent assassinations that followed the Islamic Revolution -- including dissidents and intellectuals. But the killings have been obscured by the monolithic structure of the new cleric-led government, the lack of an independent press, and a ban on nongovernmental political bodies.
Nima Rashedan is an Iranian journalist who has studied what he believes is a pattern of political assassinations. "The concern of the plotters of terrorism in the first postrevolution decade was the damage that the victims could inflict upon the foundations of the revolution in Tehran," he said. "Those who were assassinated were considered threats to the revolution, considered serious threats by fundamentalist revolutionary forces in Tehran. But in the second decade, the trend becomes somewhat more sophisticated. It seems that terror was now used as a lever in foreign policy, as a balancing or sometimes destabilizing ballast in the foreign relations of the Islamic Republic. In the second wave of assassinations -- which statistically is the larger part, under Intelligence Minister Ali Fallahian -- individuals were not as important as the very nature of terror was."
Observers suggest that it was only after the election of reformist President Mohammad Khatami in 1997 that an independent press emerged to look into cases where intellectuals or dissidents disappeared under mysterious circumstances.
The first cases to receive significant public attention were the 1998 killings of four liberal dissidents, including well-known secular politician Dariush Foruhar and his wife, Parvaneh. The outcry sparked an investigation that officially blamed "rogue" agents in the Intelligence Ministry with killing the dissidents on their own initiative. Further investigations were stymied when the accused ringleader of the agents, Said Emami, died in jail. Emami's death was labeled a suicide.
Some journalists who have investigated the killings say they appear to be part of a wider campaign of targeting dissidents, believed to have claimed the lives of 70 to 100 victims.
Many observers suspect that the so-called rogue intelligence agents were acting on orders from much higher authorities, possibly the then head of the Intelligence Ministry, Ali Fallahian. But the inconclusive nature of the investigations left such questions unanswered.
Nasser Zarafshan, a lawyer representing the families of the slain dissidents, described the case in 2001. "Mr. Fallahian, who was for years the direct superior of Saeed Emami, and therefore has had direct supervision over his work, says that, 'I will give no explanation without my superior being present.' And thus to avoid the circle of investigations to encompass him, he attaches himself to others," Zarafshan said. "Therefore, people themselves guess what's wrong with the case. The problem is not to which faction the perpetrators of the murders belong, but to which faction the issuer of the fatwas [assassination orders] belongs."
Alireza Nourizadeh is a journalist who has investigated a number of dissident deaths. He suggests that former Intelligence Ministry head Fallahian's post appears to have shielded him from more thorough scrutiny.
"In the courtyard of the Intelligence Ministry, those who later became the key players in this case were playing soccer when the minister arrived in his Mercedes-Benz. He called out to Mr. Mostafa Kazemi and asked him, 'Why hasn't this job been done?' Later, Mr. Minister fled from prosecution by taking an oath [that he was not involved], and he is now the prosecutor. But four witnesses -- two of whom I have talked to -- have admitted that the minister did come to the courtyard, called Kazemi and Alikhani, and asked them why the job was not done. It was after that talk that they started to act. They went to the Foruhars' house with the false claim that their stolen car had been found. They entered the house and brutally murdered Dariush and Parvaneh -- the latter was sick and in bed upstairs -- and even broke Foruhar's arm," Nourizadeh said.
Journalists and lawyers pressing for information have faced strong official pressure to abandon the case, and several have been imprisoned. One prominent journalist, Akbar Ganji, continues to serve a jail term.
With such unsolved cases, it remains unclear whether hard-line authorities in control of the Intelligence Ministry or other security branches are willing to resort to extrajudicial killings to silence critics.
Reformist Mohammad Reza Khatami, the brother of the Iranian president and the secretary of the Mosharekat Party, has warned that a "cancerous tumor" is still alive and could reemerge at any moment.
(The final part of this four-part series looks at how Ayatollah Khomeini's fatwa against British author Salman Rushdie continues to cloud Tehran's claims to eschew terrorism.)