In the early morning of Feb. 11, a congregation of more than 100 worshippers packed into the small St. Lidwina Catholic church in Sleman, Yogyakarta, 530 km from Jakarta, to take part in the weekly Sunday Mass.

Little more than 30 minutes of the service had passed when a young man yielding a meter-long samurai sword burst in through the main entrance and began attacking terror-stricken worshippers indiscriminately, leaving four people seriously injured as others ran for their lives before the perpetrator was shot in the leg and arrested.

The attack exposed the lingering threat from homegrown militants in a country that has largely avoided the scourge of Islamist terrorism since the collapse of Jemaah Islamiyah (JI) in the late 2000s. In the years since, several newly-formed groups along with JI’s offshoots have remained active beneath the radar, posing only a latent threat to security in the world’s most populous Muslim nation.

The risk of returning ISIS fighters from war zones in Syria, Iraq and Marawi adds an extra dimension to the threat. Returnees will be battle-hardened and trained in combat, as well as possessing tactical know-how and in some cases bomb-making skills. At least 500 Indonesians have traveled to fight alongside ISIS in Syria and Iraq while more than 30 are thought to have participated in the Marawi conflict.

An unknown number have already been deported from the Middle East, facing arrest and enrolment in compulsory deradicalization programmes upon their return home. An Indonesian foreign ministry spokesperson told reporters late last year that among 213 Indonesians deported from Turkey in 2017 were numerous individuals suspected of having joined ISIS or other extremist groups in Syria.

A spike in violent jihadist attacks has correlated with the arrival of ISIS returnees as a source of ideological inspiration in the wider region, raising fears that these groups could rise to the surface and pursue a campaign of terror reminiscent of Indonesia’s troubled past – when JI had the means to launch an unrelenting wave of mass-casualty attacks which claimed hundreds of innocent civilian lives.

The relative peace was shattered in January 2016, when a little-known band of militants affiliated to ISIS launched a co-ordinated gun and bomb assault on Jakarta’s Thamrin business district, killing four people. The shadowy group which carried-out the attack was later revealed to be Jamaah Ansharut Daulah (JAD); one of several domestic militant groups now causing growing concern to the authorities.

JAD was formed in 2015 and is thought to be composed of around 20 Indonesian extremist groups which have pledged allegiance to the ISIS leader Abu Bakr al-Baghdadi. The figurehead of JAD and alleged mastermind of the Jakarta attack, Bahrun Naim, was reportedly killed fighting alongside ISIS in Syria in December.

Another JAD leader, radical cleric Aman Abdurrahman, is currently on trial charged with helping to plan the attack. Indonesia’s national police chief Tito Karnavian warned in October that JAD ‘has structures in at least eight provinces’ and represents the biggest security threat to the country.

The authorities are also keeping a close watch on Jamaah Ansharut Tauhid (JAT). JAT was established after a cohort of militants loyal to JI co-founder Abu Bakar Ba’asyir splintered from the main organization in 2008. JAT vowed to readopt the violent tactics abandoned by JI and fight for the creation of an Islamic caliphate in Indonesia. Ba’asyir was imprisoned in 2011 for establishing a militant training camp in Aceh province, leaving the group under the control of his two sons. The group retains operational capability and is still thought to have several hundred members across Indonesia.

JAT’s parent organization, JI, has not carried out attacks for a long time, opting to focus instead on education and outreach. However, a report released last year by the Jakarta-based Institute for the Policy Analysis of Conflict (IPAC) suggested that JI is actively recruiting again and has bolstered its clandestine military wing. The latest estimates indicate JI currently has more than 1,000 members.

A jihadist threat also persists from Mujahidin Indonesia Timur (MIT), a well-established group which has now pledged allegiance to ISIS and continues to operate in parts of Java and Sulawesi, in the east of the country. Despite attempts to eliminate MIT and the high-profile killing of its enigmatic former leader Santoso in July 2016, the group has survived in its rural strongholds.

In January, Indonesia extended Operation Tinombala in central Sulawesi until June to aid the military in their efforts to capture members of the group. The operation has been ongoing for two years and has resulted in the arrest or killing of around 30 MIT members, yet has not been able to eradicate the group entirely.

While JAD, JAT and MIT pose the most visible threat to national security, many smaller radical terror cells are thought to exist across the archipelago. And since the Thamrin assault reopened the floodgates of domestic militancy, a steady stream of further – albeit lower-profile – attacks have followed in its wake.

On May 24 last year two suicide bombers detonated themselves and killed three civilians at a bus terminal in Jakarta. A month later, ISIS-inspired militants stabbed to death a police officer in the western city of Medan. On Nov. 12, two JAD members armed with bows and arrows set fire to a police station in Dharmasraya before being shot by the security forces. 2018 has already witnessed its first incident: the sword attack which injured four Yogyakarta churchgoers in February.

Aside from these small-scale attacks which slipped through the net, authorities have also disrupted ambitious plots concocted on Indonesian soil in recent years. In 2016 Indonesia’s elite police counter-terrorism unit, Detachment 88, foiled at least 15 separate plots, before last year dismantling a cell planning to bomb the Presidential Palace in Jakarta.

Police also thwarted a plot to attack President Joko Widodo last September after arresting a suspect in possession of five petrol bombs at Penggung Airport in West Java, where President Widodo was due to arrive later that day.

Last year also saw a wave of arrests and a series of deadly clashes between militants and the security forces as the authorities attempted to crack down on the rising threat from homegrown groups. In 2017 Detachment 88 apprehended 172 suspects, of whom 16 were shot dead during arrest attempts. The number of arrests rose from 163 in 2016 and 73 in 2015. In the vast majority of attacks, arrests and armed encounters last year, the authorities linked the militants involved to either JAD, JAT or MIT.

Although Indonesia has kept a lid on the threat so far, the rapidly evolving regional context makes these seemingly domestic developments appear more worrying. The arrival of ISIS in Southeast Asia – signalled by the shock five-month jihadist takeover of the southern Philippine city of Marawi last year – could inspire extremist groups in neighbouring states to forge bolder ambitions.

Meanwhile ISIS’s online propaganda videos aimed at Indonesians could boost recruitment and provoke radicalized individuals in the country to carry-out low-tech attacks, as appears to have happened in Yogyakarta.

The jihadist movement in Indonesia has reached a critical juncture. What has for a decade been a limited threat posed by a plethora of domestic groups – which the authorities have been able to keep an eye on from a safe distance – could now be morphing into something more pervasive due to the infiltration of ISIS’ warped ideology into the region. Such a scenario would not be without precedent.

Indonesia’s lawmakers are trying to keep up with the shifting pace of events. A raft of new counter-terror measures designed to support a law enforcement crackdown are currently being debated in parliament to help quell the threat in its early stages. However, in the current climate, keeping on top of the jihadist threat and suppressing homegrown militants is becoming an increasingly arduous task.

Michael Hart has researched for Action on Armed Violence (AOAV) and the International Institute for Strategic Studies (IISS). He blogs at Asia Conflict Watch.