The 2005 Helsinki agreement brought about a dramatic change for the better in terms of security – the shooting stopped. After 29 years of low-intensity conflict, a series of failed ceasefires, and a military offensive from May 2003 that resulted in hundreds of civilian deaths, the sudden end to killings was extraordinary. Violence that many predicted at various stages of the peace process did not materialise: in the months following the agreement, there were no clashes between the Free Aceh Movement (GAM) and militia, no revenge killings, and few confrontations between GAM and security forces.

The reasons for the lack of violence were the same as those that led to the agreement in the first place. One was a new government, elected in September 2004, that was committed to peace and willing to make major efforts to bring the army on board. The second was the impact of martial law, which had left GAM much weakened and eager for an exit strategy. When the agreement made it clear that they would be allowed to compete in local elections, the attractions of the non-violent option increased. Finally there was the devastating tsunami. Given the trauma so many had suffered, everyone understood that there would be no support for conflict while rebuilding and reconstruction were underway. None of these factors by themselves would have been enough to ensure a post-agreement peace, but together they were a potent disincentive for violence.

The local elections in December 2006, contrary to many predictions, were also generally peaceful. Resource-based disputes, some of them intra-GAM, led to occasional violence as time went on, with distribution of reintegration funds a particular sore point. The crime rate skyrocketed, with extortion, armed robberies and kidnappings especially prominent, some of them committed by former GAM members. In general, the short-term security mechanisms set up to monitor implementation of the Helsinki agreement worked reasonably well, but as the third year of peace neared completion, there were some clouds on the horizon.

Dispute resolution mechanisms remain in very short supply. The formal court system, poor to begin with, atrophied during the conflict, as judges and prosecutors were intimidated and courthouses burned, particularly in the districts along the east coast. The agreement brought courts back into operation but, as everywhere else in Indonesia, endemic corruption, low professionalism, and limited access are major problems.

Donors have made law enforcement a focus of post-agreement programmes, hoping to inculcate the idea of community policing in a force that was marginalised by the military during the conflict. The police unit that most Acehnese used to know and dread was the paramilitary Mobile Police Brigade, Brimob. Changing perceptions of the public toward the police was as much of a challenge as changing the attitudes of the police themselves, but intensive training, combined with the willingness of former GAM leaders at a local level to work with them seems to be producing results. While there are still sporadic reports of brutality, and corruption continues, the police have been better at responding to reported crimes than many predicted.

Security fears in the first post-agreement phase focused on GAM and the military. But demobilisation and disarmament under the Helsinki Memorandum of Understanding (MoU) proceeded smoothly, largely because of clear deadlines, good faith on both sides, and the robust mandate of the Aceh Monitoring Mission (AMM). A Commission on Security Arrangements (COSA), comprising representatives of GAM and the armed forces and chaired by the head of AMM, provided an effective forum for discussion of security concerns.

The big problem in this first phase, and one that would continue to haunt the post-agreement period, was reintegration. The initial reintegration programme was based on the idea that GAM would turn over a list of 3000 names as per the terms of the MoU and financial packets would be handed out accordingly. GAM officials resisted releasing names, ostensibly on security grounds, concerned that they could become a hit list in the event of future conflict. That was a genuine fear, given its experience with past ceasefires, but the real problem was how to divide up the money among a much larger population. The solution was to give it to commanders and hope they divided it equitably. Inevitably, it did not work and became a new source of conflict.

A further problem during the first eighteen months was the functioning of the Aceh Reintegration Board (BRA). The poorly planned and even more poorly administered BRA generated enormous problems for itself at the outset by soliciting proposals for livelihood projects from "conflict victims". When this approach resulted in a staggering volume of proposals, the BRA changed tack and proposed a community-led approach channelled through the World Bank, causing considerable anger.

A further sensitivity associated with the BRA was the government's de facto acknowledgement of the existence of militias.

To avoid accusations that it was rewarding rebels, the agency decided to give Rp.10 million (about US$1000) to 6500 militia members, otherwise known as "anti-separatist fronts" or "homeland defenders" (Pembela Tanah Air, PETA). Inclusion of militia members in the reintegration programme was probably a necessary step to avoid tensions. The Indonesian military had always denied any role in creating these fronts, but in the end, it was the district military commands that provided the names of those eligible for funding. While fears that militias, backed by intelligence operatives, could become election spoilers did not materialise, the fault line between ex-rebels and loyalists remained, particularly in Central Aceh and Bener Meriah districts. This tension resurfaced dramatically in early 2008 when five members of the KPA – (Komite Peralihan Aceh, Aceh Transition Committee, the new name for the old GAM military structure) were killed in the worst act of violence since the peace agreement was signed.

Intra-GAM problems had been brewing for some time between the old guard, based in Sweden and led by Malik Mahmud, who had headed the negotiating team in Helsinki, and the younger field-based faction, led by Irwandi Yusuf. The rift initially had few security implications, but an attack in November 2006 on Humam Hamid, the old guard's candidate for governor, raised concerns about more violence to come, particularly in Bireuen district, where the camps were locked in bitter contention.

If KPA vs militias was one source of tension and GAM factionalism another, a third was that between Aceh and the central government, as illustrated by the differences over the Law on the Governing of Aceh (LoGA). The self-government promised to Aceh in Helsinki was considerably diluted in the law, and what GAM leaders view as the unimplemented provisions of the Helsinki agreement could become the basis for resumption of conflict in the future.

No serious security problems arose during the December 2006 elections in which Acehnese voters decisively chose a GAM governor and GAM candidates in seven out of nineteen races for district heads (bupati). In the general euphoria over the results, concerns over extortion and intimidation on the part of some KPA members went largely unnoticed.

Shortly after the elections, the AMM left Aceh, leaving in its wake no agency with the same authority to resolve disputes and defuse conflict. A new body called the Communications and Coordination Forum (Forum Koordinasi dan Komunikasi , FKK), on which KPA and Indonesian military officers both sit, was set up in April 2007 as part of the Aceh desk under the Coordinating Ministry of Politics, Law and Security but its mandate was narrower. It has been a useful forum when security incidents occur, such as the March 2008 attack in Central Aceh described below. But it is less effective for resolving struggles over administrative authority between Aceh and the central government.

Most security problems in 2007 were linked to district elections or rising crime. Some of the latter was linked to gang members coming up from Medan, North Sumatra (motorcycle thefts rose 300 per cent) but much of it to ex-GAM fighters, most of whom remained unemployed. Resentment rose in the GAM rank-and-file against their former commanders, some of whom were growing rich through contracts handed out by newly elected GAM officials, and there were several incidents of grenade or other attacks on KPA members, apparently by disgruntled associates. Extortion by KPA members was also increasingly reported.

A disputed election for bupati in Southeast Aceh in December 2006, in which the notoriously corrupt incumbent was edged out by a rival, led to a string of violent acts in 2007 as efforts to install the winner were repeatedly set back. The district capital, Kutacane, was hit by riots in August, followed by a grenade and arson attacks. Similar disputes over local election results have taken place across Indonesia, but in Aceh they tend to raise additional concerns. In this case the loser, Armen Desky, whose supporters were responsible for much of the violence, had close ties to Jakarta and was a strong backer of a plan to carve two new provinces out of Aceh, Aceh Leuser Antara (ALA) and Aceh Barat Selatan (ABAS) – which would be a clear violation of the MoU. Indonesian intelligence is widely believed in Aceh to be supportive of the division, in part because the National Intelligence Agency, BIN, was involved in the partition of Papua into two provinces in 2003.

An incident in Nisam, North Aceh in March brought the Indonesian army and KPA into conflict for the first time since the elections, when Indonesian soldiers beat up 14 villagers after a KPA-orchestrated attack on four of their colleagues the day before. The four soldiers had been moonlighting as security guards to protect a local school from KPA extortion; the KPA reportedly organised a "spontaneous" attack by villagers, who beat them up, claiming they were intelligence agents. The army then retaliated with force. Such direct clashes, however, were rare. There was more concern on GAM's part about the influx into Aceh of plainclothes intelligence personnel, whom they believed were going to find ways to discredit GAM, deepen intra-GAM rifts, or more generally cause trouble in the lead-up to parliamentary elections in 2009.

As Indonesia's national day approached on 17 August, hundreds of Indonesian flags were torn down across the districts of East Aceh, North Aceh and Lhokseumawe. Police suspected local KPA members but then proceeded to beat up twelve villagers in the course of their investigation, alienating the community.

Police performance in response to security problems was mixed. Despite intensive post-conflict human rights training provided through international donors to the police, reports of brutality and petty extortion continued. And in some GAM strongholds, police reportedly felt their numbers were too few to effectively challenge KPA offenders so they did nothing. The MoU fixed the number of police in Aceh at 9100 for a population of about 4.4 million; with reinforcements, the figure in 2008 stood at about 13,000, still low.

Resentment over distribution of reintegration funds continued to fester, even after the reorganisation of BRA in April 2007, further complicated by the slow transfer of funds from Jakarta. The new head, senior GAM member Nur Djuli, scrapped the idea of community projects and returned to a policy of individual payments, focused on housing, generating new anger, this time from communities who had been promised payments.

In 2008, the killing of five KPA members, an intensified campaign for ALA and ABAS, and continuing criminal activity were the main security preoccupations.

The incident in Atu Lintang, Central Aceh, began as a struggle over control of the local bus terminal between a militia-backed group of thugs known as IPT and local KPA members. On 29 February at a meeting at the local transportation office to settle the dispute, four KPA members were attacked as they arrived. That night text messages began circulating that there was going to be war in Takengon, and both sides started mobilising truckloads of supporters. Muzakkir Manaf, the head of KPA, ordered his men not to do anything. In the early hours of 1 March, a mob of some 200 people attacked the KPA office in Atu Linge in what was clearly a premeditated and organised attack. They set it on fire, burning four to death; a fifth man was also killed. The head of the district council (also linked to the militias) claimed that people were tired of KPA extortion, as if to justify the attack.

The good news was that police swiftly arrested the ringleaders of the attack, and the KPA did not retaliate. But it was an incident very similar to this one, and in the same area, which led to the unravelling of a 2002 Cessation of Hostilities Agreement . Central Aceh and neighbouring Bener Meriah are the districts where the prospects of GAM-militia violence erupting have always been highest, in part because the militia there is one of the few with a genuine support base, rooted in reaction to GAM attacks there in 2000-2001.

The ALA and ABAS campaigns were given an unexpected boost in January 2008 when the Indonesian parliament recommended their creation. This was followed by a lobbying visit to Jakarta of 430 village heads from the prospective provinces, raising questions about who paid for their tickets. Former president and perpetual presidential contender Megawati Sukarnoputri received the delegation, saying she supported the campaign, a sign that funding from the Yudhoyono government's opponents could be channeled to it. But Governor Irwandi has made it clear he opposes the division, and any effort to go around him to bring it about could mean the torpedoing of the MoU.

Meanwhile, police claimed that the number of armed crimes was twenty-two times higher than before the Helsinki agreement was signed. On March 13, Mukhlis Gayo, the man responsible for organising the village heads' trip to Jakarta, was kidnapped in Central Aceh by an armed group led by a KPA member. Police were able to rescue him and arrest two of the kidnappers. It was the twelfth reported kidnapping in Aceh since June 2007. Then in April, five Chinese nationals were kidnapped for ransom in Gayo Lues district; the affiliation of the perpetrators as of this writing was unclear. The victims were released after ransom money was paid.

No one should take peace in Aceh for granted. Major social and political tensions remain, and as the Atu Lintang incident illustrates, it does not take much to set a spark to the kindling. But overall the level of violence has been low, and most of the incidents have not taken place along the fault lines of the old conflict between GAM and the Indonesian state. There are dangers ahead, however, particularly if political interests in Jakarta see benefits to be gained from meddling in Aceh, as in the ALA-ABAS issue. Continued misbehaviour on the part of KPA members could provide an opening for that meddling. But the vexing issue of reintegration also needs addressing. As long as ex-combatant unemployment remains high, the reintegration programme remains dysfunctional, and resentment grows over the perceived gulf between haves and have-nots, the potential for security problems remains high.