The arrest of Jemaah Islamiyah (JI) leader Para Wijayanto, a supposedly non-violent member of the regional terrorist network who has been on the run for the past 17 years, is a timely reminder that terror groups affiliated with the Islamic State (ISIS) are not the only persistent threat to Indonesia’s security.

Wijayanto, 54, was detained at a hotel in eastern Jakarta following the arrest of 12 JI members, including eight who had either gone to Syria or had been involved in sending other militants there for training with the al Qaeda-affiliated an-Nusra militia, now known as Jabhat Fatah al-Sham (JFS).

Despite JI’s professed peaceful approach, the training in Syria is a throwback to the terror outfit’s early history in the mujahedeen training camps of Afghanistan during the Russian occupation and presents another long term security risk as the radical Muslim world adjusts and adapts to the collapse of the ISIS caliphate.

Among other senior JI leaders now in custody are Taufik Teguh Prasetyo, 46, who returned from Syria in 2013, Agus Suparnoto, 43, who arranged travel to Syria, and Joko Supriyono, 47, owner of an eyeglass kiosk and a motorcycle repair shop and the coordinator of all JI training in Central Java from 2016-19.

According to Institute for Policy Analysis of Conflict (IPAC) director Sidney Jones, Wijayanto has not supported violence on Indonesian soil in recent years, presiding instead over a largely successful effort to rebuild the extremist organization through religious outreach and education.

An Indonesian man wears a jacket depicting an image of deceased al-Qaeda leader Osama bin Laden. Photo: iStock/Getty

Police claim the terrorist leader has also been trying to build an economic base, even reportedly opening palm oil plantations in Sumatra and Kalimantan as sources of funding for the establishment of a caliphate that would require a fighting force to protect.

“It’s not as though its members have abandoned jihad, only that if military operations undermine the core goal of building a base through dakwah (religious outreach) then they should be stopped and reassessed,” said Jones in a 2017 report on JI’s re-emergence.

The JI leadership rejected homegrown attacks beginning in 2007, two years after the last of four suicide bombings in Bali and Jakarta which killed 243 people, many of them Indonesian Muslims, and put the vast, ethnically-diverse archipelago squarely on the global map of Islamic terrorism.

A JI splinter group, led by Malaysian Noordin Mohammad Top, killed another seven people in the bombing of Jakarta’s neighboring JW Marriott and Ritz Carlton hotels in July 2009. He died two months later in a police raid in Central Java.

As with al Qaeda, its parent organization, JI has been a staunch opponent of ISIS, which began gaining considerable ground among Indonesian extremist groups in 2014 with the endorsement of such prominent figures as radical cleric Abu Bakar Ba’asyir, 80, widely regarded as JI’s former spiritual leader and now serving a 15 year prison term for terrorism-related activities.

Ba’asyir, who has always denied JI’s existence, formed the Indonesian Mujahedeen Council (MMI), a collection of militant groups as early as 2004, but resigned four years later saying its internal democratic structure contradicted Islam.

Muslim militant cleric Abu Bakar Bashir (C-in white) is guarded by Indonesian elite commandos as he leaves the police headquarters to undergo cataract surgery in Jakarta on February 29, 2012. Indonesia's top court on February 27 upheld a 15-year jail term against Islamist militant Abu Bakar Bashir for terrorist acts, reversing an earlier decision to slash the sentence to nine years. AFP PHOTO / ADEK BERRY / AFP PHOTO / ADEK BERRY
Abu Bakar Ba’asyir (C) leaves police headquarters to undergo cataract surgery in Jakarta in a February 29, 2012.  Photo: AFP/Adek Berry

Posing with the ISIS flag alongside other terrorist detainees, he publicly pledged allegiance to the death cult’s leader, Abu Bakr al-Baghdadi, from behind bars at the reputed high-security Nusakambangan island prison off Central Java’s southern coast.

Hundreds of Indonesian militants of all stripes travelled secretly to the Middle East to join ISIS. The Indonesian government is now weighing the best way to repatriate and rehabilitate the survivors without them posing a future threat to national security.

By then JI had fragmented under continuous pressure from the highly effective Detachment 88 counterterrorism unit. It was replaced by the emergence of other militant groups and, more recently, by at least five independent cells loyal to ISIS, which initially struggled to coordinate their operations.

That may have been one reason for the poor planning behind the gun and bomb attack carried out by the pro-ISIS Jamaah Ansharut Daulah (JAD) in downtown Jakarta in January 2016, which killed four police and civilians and all four perpetrators in scenes recorded by scores of bystanders’ mobile phones.

Jailed JAD leader Aman Abdurrahman, 47, who was pictured sitting next to Ba’asyir in a now-notorious prison photograph, was later sentenced to death for masterminding the 2016 attack. It was the first capital punishment penalty to be handed down since the 2008 execution of three perpetrators of the 2002 Bali bombing terror attack.

Armed police escort Aman Abdurrahman, leader of militant outfit Jamaah Ansharut Daulah, a group linked to the Islamic State (ISIS), to a court hearing in Jakarta on May 18, 2018.Photo: AFP / Bay Ismoyo
Police escort Jamaah Ansharut Daulah leader Aman Abdurrahman to a court hearing in Jakarta on May 18, 2018. Photo: AFP / Bay Ismoyo

Better planned and far more devastating was the series of ISIS-inspired suicide bombings directed at three churches in the port city of Surabaya in May 2018 which left 28 people dead, including 15 innocent victims and 13 attackers from three different extremist families.

The elite Detachment 88 counterterrorist unit, known for its success in dismantling much of JI’s original network, has rounded up more than 400 suspected ISIS members since the church bombings, an indication of its increasingly sophisticated surveillance skills.

Wijayanto, the West Java-born son of an air force officer who had spent most of the past two decades in Kudus, Central Java, is believed to have been JI’s emir since 2008, when he was chosen after a wave of arrests in 2007 that netted its former two most senior leaders, Abu Dujana and Zarkasih.

Although his religious knowledge was limited, the Diponegoro University engineering graduate is known for his organizational savvy, serving as head of JI’s Central Java wakalah, an administrative subdivision, in early 2000 when he took part in a short military training course in Mindanao in the Philippines.

Despite Wijayanto’s long association with JI, he was not among the list of 12 wanted suspects produced at the end of the government’s investigation into the 2002 Bali bombing, which killed over 200 mostly Western tourists. All were subsequently captured or killed.

Buildings and cars are on fire after a bomb blast in tourist site of Kuta, Bali 13 October 2002. At least 53 people including 10 foreigners, were killed when a bomb exploded in a popular nightclub on the Indonesian resort island of Bali. AFP PHOTO/ DARMA / AFP PHOTO / DARMA
The fiery aftermath of the 2002 Bali bombing. Photo: AFP/Darma

When the Syrian conflict erupted, JI began sending cadres to Syria for short-term training, along the lines of the old Afghanistan model of the 1990s, where members were taught military skills as a part of a longer term indoctrination and preparedness program to eventually create a new military wing at home.

Jones, a recognized expert on regional terrorism, says as many as 100 JI followers may have eventually gone to Syria. How many have managed to return will only become clear after the questioning of Wijayanto and the other three JI leaders, she says.

“While there is no evidence that JI has changed its calculus and still believes that violence in Indonesia is counterproductive, the concern now is that some of these returned cadre could grow frustrated by the do-nothing attitude of the leadership and form a more militant splinter,” Jones says.