In the wake of the 2002 Bali bombings, Indonesia launched a major crackdown on the terrorist group that was plaguing the country.
But 20 years on, many of those involved in Jemaah Islamiyah have now served their sentences and are free again.
And far from being obliterated, Jemaah Islamiyah (JI) is now gaining strength and becoming more professional, according to an expert.
Senior Director at the Counter-Extremism Project Dr Hans-Jakob Schindler told 9News.com.au the terror group has not yet regained its 2002-era prominence.
“There has been a steady trickle of terrorist incidents for which JI is reported to be responsible,” Dr Schindler said.
“While JI of old was attacking primarily government and security forces as well as Western targets, some of the newer JI networks seem to have learned a lesson from ISIS and are now also targeting religious and ethnic minorities in Indonesia in an apparent attempt to cause societal discord.”
JI has turned to surprising ways to generate income.
The organisation is now running palm oil farms as a means of bankrolling their terror, he said.
Indonesian police said the terror group owns farms in Kalimantan and Sumatra.
Leaders of the group are drawing an income from the farms.
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In the wake of the Bali bombings, Indonesia very effectively dismantled most cells of JI and locked up its core leadership.
But the advent of ISIS complicated things.
“First of all, the authorities had serious problems keeping some of its prisons, in particular high-security ones under control,” Dr Schindler said.
“Some of the terrorist prisoners took control of some of the prisons, even swearing allegiance to ISIS while they were in prison.”
But Dr Schindler said Indonesia’s efforts to quash JI was hampered by the justice system itself.
“The Indonesian government had to slowly release some of the JI members it had arrested after the Bali incident, simply because their sentences had finished,” Dr Schindler said.
“This led to a reinvigoration of JI in Indonesia again.”
JI’s ambition remains to install an extremist Islamist regime in Indonesia.
But Dr Schindler said there was little indication JI would be able to gain traction outside Indonesia.
