Indonesia was rocked by the Christmas Eve church bombings on December 24, 2000, that killed 18 people. Just six days later, Metro Manila in the Philippines experienced similar bombings that killed 22 people.

In 2002, a series of bombings ripped through a popular nightlife spot in Bali, Indonesia, killing more than 200 people and leaving at least another 200 wounded.

In the following years, the JW Marriott Hotel, the Philippine Stock Exchange and the consulate, all in Indonesia’s capital Jakarta, were attacked, as were other locations across Southeast Asia.

The group responsible for the attacks, and others, was Jemaah Islamiyah (JI), whose members aspired to establish a hardline Islamic state in Indonesia and across wider Southeast Asia.

Often referred to by its initials, JI was alleged to have operatives in Singapore, Malaysia, Cambodia and the Philippines, and was said to be linked to other groups, including al-Qaeda and the Moro Islamic Liberation Front (MILF) in the Philippines’ Mindanao island.

Though JI was responsible for a long list of atrocities and hundreds of casualties in the early 2000s – its last recorded attack was the bombing of a police compound in West Java province in 2011 – the group, and the fear of terror attacks, is largely forgotten in the region now.

So, how did Indonesia’s and other governments in Southeast Asia effectively curtail a regional threat while the United States-led “war on terror” left entire countries shattered and regions of the world in chaos following the September 11, 2001 attacks on the US?

“The early 2000s certainly felt dangerous at the time,” Zachary Abuza, a professor at the National War College in Washington, DC, told Al Jazeera.

“But the Bali bombing really shook Indonesia out of its complacency. The new terrorism law changed the public perception of the perceived level of danger and the authorities had free rein to do their work without political interference,” Abuza said.

‘It broke JI’s back’

At the time of the Bali bombings in late 2002, Indonesia did not have specific and targeted antiterrorism legislation, although this was quickly drafted and signed into law in 2003 and applied retroactively to some of the perpetrators of the attack on the popular holiday island.

Three senior members of JI, Imam Samudra, Ali Ghufron and Amrozi, were quickly arrested, prosecuted, and executed in 2008 for their roles in masterminding the bombings.

A fourth perpetrator, Ali Imron, was sentenced to life in prison.

In 2003, Hambali, a Malaysia-based member of JI, allegedly responsible for securing funding for the group, was arrested in Thailand after spending months hiding out in the Cambodian capital, Phnom Penh.

Renditioned by the US, Hambali was tortured at CIA “black sites” before being transferred to the US military’s notorious Guantanamo Bay detention camp in Cuba where he remains imprisoned to this day for his alleged role in the Bali bombings.

Indonesia and other governments in the region continued to close the net between JI members and their leaders.

In 2007, Abu Dujana, the head of JI’s military operations, was arrested. In 2010, Abu Bakar Bashir, the “spiritual head” of the organisation, was captured and sentenced to 15 years in prison. He was released early in January 2021.

“When people were arrested, it broke JI’s back,” Abuza said.

“But JI as an organisation still existed and the government gave it ample space to exist, allowing it to run its madrasas [Islamic educational institutions], charities and businesses,” he said.

The Indonesian government officially declared JI an illegal organisation in 2008, but authorities took a more measured approach by continuing to allow its members a degree of autonomy provided they did not engage in violence.

‘Jihad as a spiritual struggle’

According to Farihin, a member of JI based in Indonesia, the organisation remains active, although it has now changed its philosophy to one of pacifism and focuses on works such as religious teaching and other socially-minded causes.

“There is no focus on violence now,” he told Al Jazeera.

“Only on jihad as a spiritual struggle to guard against our personal sins as individuals,” he said.

“All religions have this concept in some form.”

While Farihin still describes himself as a member of JI, he said the original grouping has fractured and splintered many times over the years, owing to people having different views and opinions.

These differences of opinion are regularly cited as another reason for the success of the regional approach to the so-called “war on terror” – a mix of internal political disputes and external security operations.

By 2007, Abuza recounted, JI was “riddled by factionalism” as remaining members of the organisation jostled for power and clashed on how to create a blueprint for their operations moving forward.

“Abu Dujana had different ideas for the organisation and felt that bombing foreigners was not the way to achieve its aims,” Abuza said.

“Enough people in JI thought it was best to lie low after the Bali bombing and that the attack had not been productive,” he said.

“Abu Dujana was not arguing that killing foreigners was morally wrong, just that it was not productive as, with each attack and subsequent arrests, the organisation was getting weaker.”

Counterterrorism work continues

Indonesia also came a long way in regards to creating an effective counterterrorism framework that has significantly weakened networks of potential attackers across the region, said Alif Satria, a researcher at the department of politics and social change at the Centre for Strategic and International Studies in Indonesia.

“First is the creation of Densus 88 in 2003 through the help of other countries. This has ensured that Indonesia has a well-functioning counterterrorism unit with the necessary intelligence and operational skills to dismantle networks,” Satria told Al Jazeera.

Densus 88 or Counterterrorism Special Detachment 88, was a unit formed in 2003 under the umbrella of the National Police and was funded, equipped, and trained in part by the US and Australia.

Satria added that another milestone was the creation of Indonesia’s National Counterterrorism Agency (BNPT) in 2010.

Deradicalisation programmes led by the police in the early 2000s were also critical in ensuring that those arrested did not re-engage with hardline groups once they were released.

“As a result, Indonesia has managed to keep its recidivism rate at around 11 percent,” he said.

However, the counterterrorism work conducted by the Indonesian authorities is still in progress.

Who will emerge next?

Open-source data collection shows that between 2021 and 2023, more JI members were arrested than members of other groups such as Jamaah Ansharut Daulah (JAD), an ISIL-affiliated group responsible for recent attacks in Indonesia and the wider region.

Some of the more recent incidents include the 2018 Surabaya bombings in which three Christian churches were attacked in the city of Surabaya by a husband and wife and their four children, one of whom was just nine years old. Fifteen people were killed.

The same group was also behind the Jolo Cathedral bombings in Sulu in the Philippines in 2019 that killed 20 people.

“Between 2021 and 2023, there were some 610 people arrested, 42 percent of whom were JI and 39 percent JAD and other pro-Islamic State groups,” Satria said.

“For me, that goes to show that, despite not conducting attacks, JI is very much still active, be it in conducting recruitment, fundraising or preparing for its regeneration,” he said.

Abuza agreed with that cautious tone, saying the lack of clear leadership on a global scale for hardline groups had also contributed to a general sense of quintessence.

But that could quickly change.

“These organisations are living organisations and respond to the external environment,” Abuza said.

“Everyone is waiting to see what happens in the Middle East and who emerges as a leader,” he said.

“Someone will,” he added.