Algerian Civil War

2008/9 Schools Wikipedia Selection. Related subjects: Military History and War

Algerian Civil War
Date 1991 to 2002 Location Algeria Result Victory for Algerian government, continued insurgency by the GSPC
Belligerents
Algerian government France	Islamic Armed Movement (MIA) Islamic Salvation Army (AIS) others...	Armed Islamic Group (GIA)
Commanders
Ali Kafi Liamine Zéroual Abdelaziz Bouteflika	MIA: Abdelkader Chebouti AIS: Madani Mezrag	Antar Zouabri et al.
Strength
140,000 (1994) 124,000 (in 2001)	2,000 (1992) 40,000 (1994) 10,000 (1996) 300–1,000 (2005)	Unknown
~150,000–200,000 dead See: List of Algerian massacres

The Algerian Civil War was an armed conflict between the Algerian government and various Islamist rebel groups which began in 1991. It is estimated to have cost between 150,000 and 200,000 lives. More than 70 journalists were assassinated, either by security forces or by Islamists. The conflict effectively ended with a government victory, following the surrender of the Islamic Salvation Army and the 2002 defeat of the Armed Islamic Group. However, low-level fighting still continues in some areas.

The conflict began in December 1991, when the Islamic Salvation Front (FIS) party gained popularity amongst the Algerian people and the National Liberation Front (FLN) party, fearing the former's victory, cancelled elections after the first round. At this time the country's military effectively took control of the government, and president Chadli Bendjedid was forced from office. After the FIS was banned and thousands of its members arrested, Islamist guerrillas rapidly emerged and began an armed campaign against the government and its supporters. They formed themselves into several armed groups, principally the Islamic Armed Movement (MIA), based in the mountains, and the Armed Islamic Group (GIA), based in the towns. The guerrillas initially targeted the army and police, but some groups soon started attacking civilians. In 1994, as negotiations between the government and the FIS's imprisoned leadership reached their height, the GIA declared war on the FIS and its supporters, while the MIA and various smaller groups regrouped, becoming the FIS-loyalist Islamic Salvation Army (AIS).

Soon after, the talks collapsed, and new elections, the first since the 1992 coup d'état, were held—won by the army's candidate (himself a former active participant, as were a significant number of other military officials, in president Bendjedid's FLN government), General Liamine Zéroual. Conflict between the GIA and AIS intensified. Over the next few years, the GIA began a series of massacres targeting entire neighborhoods or villages; some evidence also suggests the involvement of government forces. These massacres peaked in 1997 around the parliamentary elections, which were won by a newly created pro-Army party, the National Democratic Rally (RND). The AIS, under attack from both sides, opted for a unilateral ceasefire with the government in 1997, while the GIA was torn apart by splits as various subdivisions objected to its new massacre policy. In 1999, following the election of a new president, Abdelaziz Bouteflika, a new law gave amnesty to most guerrillas, motivating large numbers to "repent" (as it was termed) and return to normal life. The violence declined substantially, with effective victory for the government. The remnants of the GIA proper were hunted down over the next two years, and had practically disappeared by 2002.

A splinter group of the GIA, the Salafist Group for Preaching and Combat (GSPC), initially based on the fringes of Kabylie, formed in 1998 to dissociate itself from the massacres. However, despite its former repudiation of attacking non-combatants, they "...eventually returned to killing civilians" and in October of 2003, publicly endorsed Al-Qaeda. The GSPC rejected the amnesty and has continued to fight, although many individual members have surrendered. While as of 2006, its comparatively sparse activities - mainly in mountainous parts of the east - are the only remaining fighting in Algeria, a complete end to the violence is not yet in sight.

Liberalization: Prelude to war

By the end of 1987, the single-party socialist republic under which Algeria had fared relatively well since the 1960s no longer seemed viable. The government had relied heavily on high oil prices, and when, in 1986, oil prices went from $30 to $10 a barrel, the planned economy came under severe strain, with shortages and unemployment rife. In October 1988 (" Black October"), massive demonstrations against President Chadli Bendjedid took place throughout Algerian cities, with an Islamist element prominent among the demonstrators. The army fired on the demonstrators, leaving some dead and shocking many.

The president's response was to make moves towards reform. In 1989, he brought in a new constitution which disestablished the ruling party, the National Liberation Front (FLN), and made no mention of socialism, while promising "freedom of expression, association, and assembly". By the end of the year, a variety of political parties were being established and recognized by the government—among them, the Islamic Salvation Front (FIS).

The FIS incorporated a broad spectrum of Islamist opinion, exemplified by its two leaders. Its president, Abbassi Madani, a professor and ex-independence fighter, represented a relatively moderate religious conservatism and symbolically connected the party to the Algerian War of Independence, the traditionally emphasized source of the ruling FLN's legitimacy; he expressed tepid support for the concept of democracy and rejected the idea that it could override the sharia. The vice-president, Ali Belhadj, a younger and less educated Algiers preacher who had already played a significant role in the October demonstrations, made aggressively radical speeches that rallied dissatisfied lower-class youth and alarmed non-Islamists with his clear-cut rejection of democracy and what they considered his repressive views on women. In February 1989, for example, Belhadj stated:

There is no democracy because the only source of power is Allah through the Koran, and not the people. If the people vote against the law of God, this is nothing other than blasphemy. In this case, it is necessary to kill the non-believers for the good reason that they wish to substitute their authority for that of God.

The FIS rapidly became by far the biggest Islamist party, with a huge following concentrated especially in large urban areas. In 1990 they swept the local elections with 54% of votes cast. The Gulf War further energized the party, as it outdid the government in gestures opposing Desert Storm.

In May 1991, the FIS called for a general strike to protest the government's redrawing of electoral districts, which it saw as a form of gerrymandering. The strike itself was a failure, but the huge demonstrations the FIS organized in Algiers were effective; the FIS was persuaded in June to call the strike off by the promise of fair parliamentary elections. Shortly afterwards, the increasingly alarmed government arrested Madani and Belhadj, along with a number of lower-ranking members. The party, however, remained legal, and passed to the effective leadership of Abdelkader Hachani.

The rise of the party continued. It eventually agreed to participate in the next elections, after expelling dissenters, such as Said Mekhloufi, who advocated direct action against the government. In late November, armed Islamists connected to the extremist Takfir wal Hijra attacked a border post at Guemmar, foreshadowing the conflict to come; otherwise, an uneasy calm prevailed. On December 26, the FIS handily won the first round of parliamentary elections; with 48% of the overall popular vote, they won 188 of the 232 seats decided and an FIS government seemed inevitable.

Elections cancelled: a guerrilla war begins

     FIS majority     50% FIS     non-FIS majority     Undecided     No data availableIn the above provincial seat allocation results of the 1991 elections, the FIS attained majorities in most of Algeria's populated areas.

The army saw this outcome as unacceptable. The FIS had made open threats against the ruling pouvoir, condemning them as unpatriotic and pro-French, as well as financially corrupt. Additionally, FIS leadership was at best divided on the desirability of democracy, and some expressed fears that a FIS government would be, as U.S. Assistant Secretary of State Edward Djerejian put it, "one man, one vote, one time."

On January 11, 1992 the army cancelled the electoral process, forcing President Chadli Bendjedid to resign and bringing in the exiled independence fighter Mohammed Boudiaf to serve as a new president. So many FIS members were arrested — 5,000 by the army's account, 30,000 according to FIS, and including Abdelkader Hachani — that the jails had insufficient space to hold them in; camps were set up for them in the Sahara desert, and bearded men feared to leave their houses lest they be arrested as FIS sympathizers. A state of emergency was declared, and many ordinary constitutional rights were suspended. Any protests that occurred were suppressed, and human rights organizations, such as Amnesty International, reported frequent government use of torture and holding of suspects without charge or trial. The government officially dissolved the FIS on March 4.

Of the few FIS activists that remained free, many took this as a declaration of war. Throughout much of the country, remaining FIS activists, along with some Islamists too radical for FIS, took to the hills with whatever weapons were available and became guerrilla fighters. Their first attacks on the security forces (not counting the Guemmar incident) began barely a week after the coup, and soldiers and policemen rapidly became targets. As in previous wars, the guerrillas were almost exclusively based in the mountains of northern Algeria, where the forest and scrub cover were well-suited to guerrilla warfare, and in certain areas of the cities; the very sparsely populated but oil-rich Sahara would remain mostly peaceful for almost the entire duration of the conflict. This meant that the government's principal source of money—oil exporting—was largely unaffected.

The tense situation was compounded by the economy, which collapsed even further that year, as almost all of the longstanding subsidies on food were eliminated. The hopes many placed in the seemingly untainted figure of Boudiaf were soon dashed when he fell to a bullet from one of his own security guards in late June. Soon afterwards, Abbassi Madani and Ali Belhadj were sentenced to 12 years in prison.

By August 26 it had become apparent that some guerrillas were beginning to target civilians as well as government figures: the bombing of the Algiers airport claimed 9 lives and injured 128 people. The FIS condemned the bombing along with the other major parties, but the FIS's influence over the guerrillas turned out to be limited.

The initial fighting appears to have been led by the small extremist group Takfir wal Hijra and associated ex-Afghan fighters. However, the first major armed movement to emerge, starting almost immediately after the coup, was the Islamic Armed Movement (MIA). It was led by the ex-soldier Abdelkader Chebouti, a longstanding Islamist who had kept his distance from the FIS during the electoral process. In February 1992, ex-soldier, ex-Afghan fighter, and former FIS head of security Said Mekhloufi founded the Movement for an Islamic State (MEI). The various groups arranged several meetings to attempt to unite their forces, accepting the overall leadership of Chebouti in theory. At the last of these, at Tamesguida on September 1, Chebouti expressed his concern about the movement's lack of discipline, in particular worrying that the Algiers airport attack, which he had not approved, could alienate supporters. Takfir wal Hijra and the Afghans (led by Noureddine Seddiki) responded by agreeing to join the MIA. However, the meeting was broken up by an assault from the security forces, provoking suspicions which prevented any further meetings.

The FIS itself established an underground network, with clandestine newspapers and even an MIA-linked radio station, and began issuing official statements from abroad starting in late 1992. However, at this stage the opinions of the guerrilla movements on the FIS were mixed; while many supported FIS, a significant faction, led by the "Afghans", regarded party political activity as inherently un-Islamic, and therefore rejected FIS statements.

In January 1993, Abdelhak Layada declared his group independent of Chebouti's. The new faction was called the Armed Islamic Group (GIA, from French Groupe Islamique Armé). It became particularly prominent around Algiers and its suburbs, in urban environments. It took a hardline position, opposed to both the government and the FIS, affirming that "political pluralism is equivalent to sedition" and issuing death threats against several FIS and MIA leaders. It was far less selective than the MIA, which insisted on ideological training; as a result, it was regularly infiltrated by the security forces, resulting in a rapid leadership turnover as successive heads were killed.

In 1993, the divisions within the guerrilla movement became more distinct. The MIA and MEI, concentrated in the maquis, attempted to develop a military strategy against the state, typically targeting the security services and sabotaging or bombing state institutions. From its inception on, however, the GIA, concentrated in urban areas, called for and implemented the killing of anyone supporting the authorities, including government employees such as teachers and civil servants. It assassinated journalists and intellectuals (such as Tahar Djaout), saying that "The journalists who fight against Islamism through the pen will perish by the sword.". It soon stepped up its attacks by targeting civilians who refused to live by their prohibitions, and later in 1993 began killing foreigners, declaring that "anyone who exceeds that period [a one-month deadline] will be responsible for his own sudden death." After a few conspicuous killings, virtually all foreigners left the country; indeed, (often illegal) Algerian emigration too rose substantially, as people sought a way out. At the same time, the number of visas granted to Algerians by other countries began to drop substantially.

Failed negotiations and guerrilla infighting

The violence continued throughout 1994, although the economy began to improve during this time; following negotiations with the IMF, the government succeeded in rescheduling debt repayments, providing it with a substantial financial windfall, and further obtained some 40 billion francs from the international community to back its economic liberalization. As it became obvious that the fighting would continue for some time, General Liamine Zéroual was named new president of the High Council of State; he was considered to belong to the dialoguiste (pro-negotiation) rather than éradicateur ( eradicator) faction of the army. Soon after taking office, he began negotiations with the imprisoned FIS leadership, releasing some prisoners by way of encouragement. The talks split the political spectrum; the largest political parties, especially the socialist FLN and Kabyle socialist FFS, continued to call for compromise, while other forces—most notably the General Union of Algerian Workers (UGTA), but including smaller leftist and feminist groups such as the ultra-secularist RCD—sided with the "eradicators". A few shadowy pro-government paramilitaries, such as the Organisation of Young Free Algerians (OJAL), emerged and began attacking civilian Islamist supporters. On March 10, 1994, over 1000 (mainly Islamist) prisoners escaped Tazoult prison in what appeared to be a major coup for the guerrillas; later, conspiracy theorists would suggest that this had been staged to allow the security forces to infiltrate the GIA.

Meanwhile, under Cherif Gousmi (its leader since March), the GIA became the most high-profile guerrilla army in 1994. In May, the FIS suffered an apparent blow as several of its leaders that were not jailed, along with the MEI's Said Makhloufi, joined the GIA; since the GIA had been issuing death threats against them since November 1993, this came as a surprise to many observers, who interpreted it either as the result of intra-FIS competition or as an attempt to change the GIA's course from within. On August 26, the GIA even declared a caliphate, or Islamic government, for Algeria, with Gousmi as " Commander of the Faithful". However, the very next day, Said Mekhloufi announced his withdrawal from the GIA, claiming that the GIA had deviated from Islam and that this caliphate was an effort by ex-FIS leader Mohammed Said to take over the GIA. The GIA continued attacks on its usual targets, notably assassinating artists, such as Cheb Hasni, and in late August added a new practice to its activities: threatening insufficiently Islamist schools with arson.

FIS-loyal guerrillas, threatened with marginalization, attempted to unite their forces. In July 1994, the MIA, together with the remainder of the MEI and a variety of smaller groups, united as the Islamic Salvation Army (a term that had previously sometimes been used as a general label for pro-FIS guerrillas), declaring their allegiance to FIS and thus strengthening FIS's hand in the negotiations. By the end of 1994, they controlled over half the guerrillas of the east and west, but barely 20% in the centre, near the capital, which was where the GIA were mainly based. They issued communiqués condemning the GIA's indiscriminate targeting of women, journalists and other civilians "not involved in the repression", and attacked the GIA's school arson campaign.

At the end of October, the government announced the failure of its negotiations with the FIS. Instead, Zéroual embarked on a new plan: he scheduled presidential elections for 1995, while promoting "eradicationists" such as Lamari within the army and organizing "self-defense militias" in villages to fight the guerrillas. The end of 1994 saw a noticeable upsurge in violence. Over 1994, Algeria's isolation deepened; most foreign press agencies, such as Reuters, left the country this year, while the Moroccan border closed and the main foreign airlines cancelled all routes. The resulting gap in news coverage was further worsened by a government order in June banning Algerian media from reporting any terrorism-related news not covered in official press releases.

A few FIS leaders, notably Rabah Kebir, had escaped into exile abroad. Upon the invitation of the Rome-based Community of Sant’Egidio, in November 1994, they began negotiations in Rome with other opposition parties, both Islamist and secular (FLN, FFS, FIS, MDA, PT, JMC). They came out with a mutual agreement on January 14, 1995: the Sant'Egidio platform. This presented a set of principles: respect for human rights and multi-party democracy, rejection of army rule and dictatorship, recognition of Islam, Arab and Berber ethnic identity as essential aspects of Algeria's national identity, demand for the release of FIS leaders, and an end to extrajudicial killing and torture on all sides. To the surprise of many, even Ali Belhadj endorsed the agreement, which meant that the FIS had returned into the legal framework, alongside with the other opposition parties. However, a crucial signatory was missing: the government itself. As a result, the platform's effect was at best limited - though some argue that, in the words of Andrea Riccardi who brokered the negotiations for the Community of Sant’Egidio, “the platform made the Algerian military leave the cage of a solely military confrontation and forced them to react with a political act”, the 1995 presidential elections. The next few months saw the killing of some 100 Islamist prisoners in the Serkadji prison mutiny, and a major success for the security forces in battle at Ain Defla, resulting in the deaths of hundreds of guerrilla fighters.

Cherif Gousmi was eventually succeeded by Djamel Zitouni as GIA head. Zitouni extended the GIA's attacks on civilians to French soil, beginning with the hijacking of Air France Flight 8969 at the end of December 1994 and continuing with several bombings and attempted bombings throughout 1995. In Algeria itself, he continued likewise, with car bombs and assassinations of musicians, sportsmen, and unveiled women, as well as the usual victims. Even at this stage, the seemingly counterproductive nature of many of its attacks led to speculation (encouraged by FIS members abroad) that the group had been infiltrated by Algerian secret services. The region south of Algiers, in particular, came to be dominated by the GIA, who called it the "liberated zone". Later, it would come to be known as the " Triangle of Death".

Reports of battles between the AIS and GIA increased, and the GIA reiterated its death threats against FIS and AIS leaders, assassinating a co-founder of the FIS, Abdelbaki Sahraoui, in Paris. At this point, foreign sources estimated the total number of guerrillas to be about 27,000.

Politics resume, militias emerge

Following the breakdown of negotiations with the FIS, the government decided to hold presidential elections. On November 16, 1995, Liamine Zéroual was elected president with 60% of votes cast. The election, contested by many candidates, including the Islamists Mahfoud Nahnah (25%) and Noureddine Boukrouh (<4%) and the secularist Said Sadi (10%), but excluding FIS, enjoyed a high turnout (officially 75%, a number confirmed by most observers) despite the FIS, FFS and FLN's call for a boycott and the GIA's threats to kill anyone who voted (using the slogan "one vote, one bullet"). A high level of security was maintained, with massive mobilization during the period immediately leading up to election day. Foreign observers from the Arab League, the UN and the Organization of African Unity voiced no major reservations. While some cried foul, the elections were generally perceived by foreigners as quite free, and the results were considered reasonably plausible, given the limited choices available.

The results reflected various popular opinions, ranging from support for secularism and opposition to Islamism to a desire for an end to the violence, regardless of politics. Hopes grew that Algerian politics would finally be normalized. Zéroual followed this up by pushing through a new constitution in 1996, substantially strengthening the power of the president and adding a second house that would be partly elected and partly appointed by the president. In November 1996, the text was passed by a national referendum; while the official turnout rate was 80%, this vote was unmonitored, and the claimed high turnout was considered by most to be implausible.

The government's political moves were combined with a substantial increase in the pro-government militias' profile. "Self-defense militias", often called "Patriots" for short, consisting of trusted local citizens trained by the army and given government weapons, were founded in towns near areas where guerrillas were active, and were promoted on national TV . The program was received well in some parts of the country, but was less popular in others; it would be substantially increased over the next few years, particularly after the massacres of 1997.

The election results were a setback for the armed groups, who saw a significant increase in desertions immediately following the elections. The FIS' Rabah Kebir responded to the apparent shift in popular mood by adopting a more conciliatory tone towards the government, but was condemned by some parts of the party and of the AIS. The GIA was shaken by internal dissension; shortly after the election, its leadership killed the FIS leaders who had joined the GIA, accusing them of attempting a takeover. This purge accelerated the disintegration of the GIA: Mustapha Kartali, Ali Benhadjar and Hassan Hattab's factions all refused to recognize Zitouni's leadership starting around late 1995, although they would not formally break away until later. In December, the GIA killed the AIS leader for central Algeria, Azzedine Baa, and in January pledged to fight the AIS as an enemy; particularly in the west, full-scale battles between them became common.

Massacres and reconciliation

In July 1996 GIA leader Djamel Zitouni was killed by one of the breakaway ex-GIA factions and was succeeded by Antar Zouabri, who would prove an even bloodier leader.

Parliamentary elections were held on June 5, 1997. They were dominated by the National Democratic Rally (RND), a new party created in early 1997 for Zéroual's supporters, which got 156 out of 380 seats, followed mainly by the MSP (as Hamas had been required to rename itself) and the FLN at over 60 seats each. Views on this election were mixed; most major opposition parties filed complaints, and the success of the extremely new RND raised eyebrows. The RND, FLN and MSP formed a coalition government, with the RND's Ahmed Ouyahia as prime minister. There were hints of a softening towards FIS: Abdelkader Hachani was released, and Abbassi Madani moved to house arrest.

Massacres of over 50 people in the years 1997 and 1998

At this point, however, a new and vital problem emerged. Starting around April (the Thalit massacre), Algeria was wracked by massacres of intense brutality and unprecedented size; previous massacres had occurred in the conflict, but always on a substantially smaller scale. Typically targeting entire villages or neighborhoods and disregarding the age and sex of victims, GIA guerrillas killed tens, and sometimes hundreds, of civilians at a time. These massacres continued through the end of 1998, changing the nature of the political situation considerably. The areas south and east of Algiers, which had voted strongly for FIS in 1991, were hit particularly hard; the Rais and Bentalha massacres in particular shocked worldwide observers. Pregnant women were sliced open, children were hacked to pieces or dashed against walls, men's limbs were hacked off one by one, and, as the attackers retreated, they would kidnap young women to keep as sex slaves. Although this quotation by Nesroullah Yous, a survivor of Bentalha, may be an exaggeration, it expresses the apparent mood of the attackers:

"We have the whole night to rape your women and children, drink your blood. Even if you escape today, we'll come back tomorrow to finish you off! We're here to send you to your God!"

The GIA's responsibility for these massacres is undisputed; it claimed credit for both Rais and Bentalha (calling the killings an "offering to God" and the victims "impious" supporters of tyrants in a press release), and its policy of massacring civilians was cited by the Salafist Group for Preaching and Combat as one of the main reasons it split off from the GIA. At this stage, it had apparently adopted a takfirist ideology, believing that practically all Algerians not actively fighting the government were corrupt to the point of being kafirs, and could be killed righteously with impunity; an unconfirmed communiqué by Zouabri had stated that "except for those who are with us, all others are apostates and deserving of death." In some cases, it has been suggested that the GIA were motivated to commit a massacre by a village's joining the Patriot program, which they saw as evidence of disloyalty; in others, that rivalry with other groups (e.g., Mustapha Kartali's breakaway faction) played a part.

According to reports by Amnesty International and Human Rights Watch army barracks were stationed within a few hundred meters of the villages, yet did nothing to stop the killings. At about the same time, a number of people claiming to be defectors from the Algerian security services (such as Habib Souaidia), having fled to Western countries, alleged that the security services had themselves committed some of the massacres. These and other details raised suspicions that the state was in some way collaborating with, or even controlling parts of, the GIA (particularly through infiltration by the secret services) - a theory popularised by Nesroullah Yous, and FIS itself. This suggestion provoked furious reactions from some quarters in Algeria, and has been rejected by many academics, though others regard it as plausible. In contrast, Algerians such as Zazi Sadou, have collected testimonies by survivors that their attackers were unmasked and were recognised as local radicals - in one case even an elected member of the FIS. Robert D. Kaplan, writing in The Atlantic Monthly, dismissed insinuations of government involvement in the massacres; "To people who had been watching Algeria's evolution, the assumption that sinister complicities within the Algerian state were involved in the assassinations and massacres was libelous." However, as Dr Youcef Bouandel notes; "Regardless of the explanations one may have regarding the violence, the authorities credibility has been tarnished by its non-assistance to endangered civilian villagers being massacred in the vicinity of military barracks."

The AIS, which at this point was engaged in an all-out war with the GIA as well as the government, found itself in an untenable position. The GIA seemed a more immediately pressing enemy, and AIS members expressed fears that the massacres—which it had condemned more than once—would be blamed on them. On September 21, 1997, the AIS' head, Madani Mezrag, ordered a unilateral and unconditional ceasefire starting October 1, in order to "unveil the enemy that hides behind these abominable massacres." The AIS thus largely took itself out of the political equation, reducing the fighting to a struggle between the government, the GIA, and the various splinter groups that were increasingly breaking away from the GIA. Ali Benhadjar's FIS-loyalist Islamic League for Da'wa and Jihad (LIDD), formed in February 1997, allied itself with the AIS and observed the same ceasefire. Over the next three years, the AIS would gradually negotiate an amnesty for its members.

GIA destroyed, GSPC continues

After receiving much international pressure to act, the EU sent two delegations, one of them led by Mário Soares, to visit Algeria and investigate the massacres in the first half of 1998; their reports condemned the Islamist armed groups. Towns soon became safer, although massacres continued in rural areas. The GIA's policy of massacring civilians had already caused a split among its commanders, with some rejecting the policy; on September 14, 1998, this disagreement was formalized with the formation of the Salafist Group for Preaching and Combat (GSPC), based in the mountains west of Kabylie and led by Hassan Hattab.

Abdelaziz Bouteflika, President of Algeria since 1999.

On September 11, Zéroual surprised observers by announcing his resignation. New elections were arranged, and on April 15, 1999, the army-backed ex-independence-fighter Abdelaziz Bouteflika was elected president with, according to the authorities, 74% of the votes. All the other candidates had withdrawn from the election shortly before, citing fraud concerns. Bouteflika continued negotiations with the AIS, and on June 5 the AIS agreed, in principle, to disband. Bouteflika followed up this success for the government by pardoning a number of Islamist prisoners convicted of minor offenses and pushing the Civil Harmony Act through parliament, a law allowing Islamist fighters not guilty of murder or rape to escape all prosecution if they turn themselves in. This law was finally approved by referendum on September 16, 1999, and a number of fighters, including Mustapha Kartali, took advantage of it to give themselves up and resume normal life—sometimes angering those who had suffered at the hands of the guerrillas. FIS leadership expressed dissatisfaction with the results, feeling that the AIS had stopped fighting without solving any of the issues; but their main voice outside of prison, Abdelkader Hachani, was assassinated on November 22. Violence declined, though not stopping altogether, and a sense of normality started returning to Algeria.

The AIS fully disbanded after January 11, 2000, having negotiated a special amnesty with the government. The GIA, torn by splits and desertions and denounced by all sides even in the Islamist movement, was slowly destroyed by army operations over the next few years; by the time of Antar Zouabri's death in early 2002, it was effectively incapacitated. The government's efforts were given a boost in the aftermath of the September 11, 2001 attacks; United States sympathy for Algeria's government increased, and was expressed concretely through such actions as the freezing of GIA and GSPC assets and the supply of infrared goggles to the army.

With the GIA's decline, the GSPC was left as the most active rebel group, with about 300 fighters in 2003. It continued a campaign of assassinations of police and army personnel in its area, and also managed to expand into the Sahara, where its southern division, led by Amari Saifi (nicknamed "Abderrezak el-Para", the "paratrooper"), kidnapped a number of German tourists in 2003, before being forced to flee to sparsely populated areas of Mali, and later Niger and Chad, where he was captured. By late 2003, the group's founder had been supplanted by the even more radical Nabil Sahraoui, who announced his open support for al-Qaeda, thus strengthening government ties between the U.S. and Algeria. He was reportedly killed shortly afterwards, and was succeeded by Abou Mossaab Abdelouadoud in 2004.

2004 presidential election and the amnesty

The release of FIS leaders Madani and Belhadj in 2003 had no observable effect on the situation, illustrating a newfound governmental confidence which would be deepened by the 2004 presidential election, in which Bouteflika was reelected by 85% with support from two major parties and one faction of the third major party. The vote was seen as confirming strong popular support for Bouteflika's policy towards the guerrillas and the successful termination of large-scale violence.

In September 2005 a national referendum was held on an amnesty proposal by Bouteflika's government, similar to the 1999 law, to end legal proceedings against individuals who were no longer fighting, and to provide compensation to families of people killed by government forces. The controversial Charter for Peace and National Reconciliation was declared to have won with 97% support, and with 80% of participation. The conditions of the campaign in Algeria were criticized in the French press, in particular in Le Monde and L'Humanité.

Lawyer Ali Merabet, for example, founder of Somoud, a NGO which represents the families of the disappeared, was opposed to the Charter which would “force the victims to grant forgiveness”. He remains wary that the time of the FIS has truly ended and notes that while people no longer support them, the project of the FIS - which he denies is Islamic - still exists and remains a threat.

The proposal was implemented by Presidential decree in February 2006, and adopted on September 29, 2006. Particularly controversial was its provision of immunity against prosecution to surrendered ex-guerrillas (for all but the worst crimes) and Army personnel (for any action "safeguarding the nation".) According to Algerian paper El Khabar, over 400 GSPC guerrillas surrendered under its terms; estimates of the GSPC's size in 2005 had ranged from 300 to 1000. The International Federation of Human Rights (FIDH) has opposed the amnesty

The fighting has continued to die down but a state of emergency remains in place. Elements within the FLN have suggested changing the constitution to allow Bouteflika to run for a third term.