This commentary is published in coordination with the 2025 Global Security Forum, of which Defense One is a media partner.
The leaders of Jemaah Islamiyah disbanded their al-Qaeda-affiliated jihadist group last June—but the schools that serve as the group’s ideological factories remain active. The Indonesian government must take action to prevent JI members who traveled to fight in Syria from using the schools to galvanize the group’s resurgence.
JI had long relied on Islamic boarding schools, or pesantren, operating under the radar as part of the Indonesian educational system. These radicalized schools steeped young minds in radical beliefs and produced a steady supply of supporters.
At least 16 former JI fighters are now in Syria, where they fought alongside the Hay’at Tahrir al-Sham rebels who overthrew the Assad regime. If they return to Indonesia, they could use the schools to galvanize the group’s return—threatening Indonesia and beyond.
The Indonesian government must take a two-pronged approach: reform the pesantren network and implement a controlled-repatriation program for such men.
First, the government must establish a dedicated regulatory body to monitor and audit pesantren. This body would ensure that extremist teachings are eliminated, replacing them with civic education and democratic values. The teachers themselves must also be vetted to ensure that they hold only moderate Islamic views, and some may need retraining.
The government must also work to involve community leaders, including religious scholars and civil society organizations, in countering extremist narratives and providing alternative educational opportunities. By building strong relationships within local communities, Indonesia can create an environment that discourages extremism and encourages moderation, helping to deradicalize those within pesantren and prevent future generations from falling prey to extremist ideologies.
At the same time, the government must also forge a controlled legal process to repatriate members of terrorist groups who went abroad to fight in conflict zones like Syria. These individuals bring battlefield experience, hardened ideologies, and critical connections to global jihadist networks. If allowed to return unchecked, they could re-join radical elements in Indonesia, revitalizing the JI movement. These returnees may serve as bridges between local militants and international jihadist networks, further complicating counterterrorism efforts.
So these fighters must be held accountable for any crimes they may have committed, but must also be given the tools to reintegrate into society in a positive way. That includes participation in rehabilitation and de-radicalization programs designed to address the causes of their extremism.
Fortunately, Indonesia can draw on other countries’ experience, adapting approaches as necessary. Saudi Arabia’s reforms in religious education and Malaysia’s initiatives for rehabilitation offer valuable lessons that Indonesia can adapt to its unique context. Egypt and Kazakhstan also have valuable experience. International cooperation and the exchange of best practices are essential.
Reforming pesantren and implementing a controlled repatriation process for foreign fighters are critical steps to secure Indonesia’s future against radicalization and violent extremism.
A comprehensive approach that combines regulatory oversight, educational reform, community engagement, and law enforcement will help eliminate JI’s ideological influence and prevent returning fighters from reigniting extremist networks that could threaten Indonesia, the region, and the world.
Dr. Noor Huda Ismail is a Visiting Fellow at the S. Rajaratnam School of International Studies at Nanyang Technological University in Singapore and an adjunct professor at International Relations Department at Diponegoro University in Central Java, Indonesia
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