Thousands of innocents died, often victims of barbarous brutality, and thousands more simply disappeared. The Armed Islamic Group (GIA) launched a campaign of civilian massacres, sometimes slitting the throats of entire villages.
It was 30 January 1997 when the security forces came for Naseera Dutour's son, Amin, in the middle of Ramadan. She has neither seen nor heard of him since. Her search for Amin took her to Algeria's notorious al-Barataki police station.
"This policeman told me: 'If you know someone highly placed, tell them to get your son out of here, otherwise he'll be taken to a place where you will never see him again.' For each individual case of disappearance we want justice and truth. And for this task we have a duty to keep up the memory of those who disappeared," Dutour said.
Outside the government's human rights office in Algiers, a large crowd of women demands that the government reveal the fate of "the disappeared". "What have they done with our children," they chant, "where have our children gone?"
Like many Algerians, they are in mixed mind about President Abdelaziz Bouteflika's referendum. They welcome any steps that bring the country closer to peace but are angry that there is no promise of investigations into the atrocities and disappearances of the past.
As speaker for the Disappeared People Committee, Naseera Dutour is among those leading the demands for justice. She was among those to address the rally.
"Give us justice, give us the truth. I want the truth. They took them away from us," Datour said.
The amnesty, if approved in the referendum, will end judicial proceedings for all those who lay down their weapons, as long as they were not involved in massacres, rapes, and bombings of public places.
But, more controversially, it absolves the state of any responsibility for the disappearances.
It is this that alarms the families of the disappeared and has prompted the international human rights organization, Amnesty International, to express fear that this could be a "final denial of truth and justice to hundreds of thousands of victims and their families."
The government of President Bouteflika hopes that the referendum will put an end to the civil war and allow it to concentrate on the task of building the state.
The violence has eased under Bouteflika's administration but the insurgency is still far from defeated.
Its origins date back to 1992, when the military cancelled national elections just as the Islamic Salvation Front was poised to win. The decision forced political Islam underground and triggered the civil war.
Bouteflika has made clear though that there can be no way back into politics for the Islamic Salvation Front.
The Algerian experience is being closely watched by governments all over the Middle East -- and elsewhere besides. Bouteflika’s government is not alone in fearing the consequences of allowing Islamic parties the right to contest elections freely -- or in questioning whether Islam and democracy are compatible. What will happen, they ask, if a radical Islamic party comes to power?
The experience of Algeria, though, illustrates the pitfalls of trying to eliminate political Islam by force.