But the capture of such big-name figures as Mr. Patek – the Javanese-Arab is believed to have participated in the 2002 Bali bombings and to have served as a key link between Al Qaeda and its Southeast Asian ally, Jemaah Islamiyah (JI) – are becoming increasingly rare.
Since 2002, Indonesian authorities have captured or killed many of the top militants operating in the country amid a successful crackdown on large terrorist groups such as JI.
That success, however, hasn't ended the threat posed by the country's extremists. It's merely atomized it, security specialists say, fueling the rise of smaller splinter groups and forcing large groups such as JI to do more networking than plotting.
Large bombing campaigns aimed at foreigners have given way to smaller-scale instances of politically and religiously motivated violence targeting locals. And the changes are forcing Indonesia to focus more on combating the root causes of extremism.
"We’re seeing much more activity on the part of small groups of seven to 10 people rather than the JI or JAT [Jamaah Ansharut Tauhid],” says Sidney Jones, a senior analyst at the International Crisis Group.
The rise of splinter cells
JAT is, according to the International Crisis Group, an above-ground organization made up of individuals with known ties to fugitive extremists and members of JI. But it was formed by imprisoned radical cleric Abu Bakar Bashir, who faces terrorism charges for allegedly helping set up and fund a militant training camp in Aceh that gave birth to a terror cell led by Abdullah Sonota, whom police arrested last June. Mr. Bashir has also been implicated in providing weapons to a group that robbed a bank in Medan, Sumatra, allegedly in search of funds for jihad.
The small group that led the robbery is a configuration of former criminals and individuals who attended JI teachings, says Noor Huda Ismail, a former student of Bashir’s who now works on reforming accused terrorists.
JI itself is a waning presence here. While the militant Islamic organization was behind dozens of large-scale attacks between 1999 and 2004, its last successful operation was the 2009 hotel bombings in Jakarta.
Because of the crackdown, the role of JI and JAT in Indonesia today has morphed into providing networking opportunities in the form of jihadist book launches and regular religious study sessions that enable small splinter groups to form, says Ms. Jones. Some remain connected to JAT or JI, but many have also formed independent breakaway cells.
As the makeup of extremist cells has mutated, so, too, has the violence, from big bombing campaigns aimed at foreigners to small-scale killings targeting locals. Victims have included non-Muslim groups and police, which analysts suspect is out of revenge for recent arrests.
Seven terror suspects were arrested in January in Klaten, Central Java, for allegedly planting homemade bombs in front of two police posts and a Roman Catholic shrine. A series of recent parcel bombs appeared to target a liberal Islamic teacher and a former counterterrorism official. Muslim mobs in February killed three members of the Ahmadiyah, a minority Islamic sect that some mainstream Muslims consider heretical.
Can the government adjust?
Now, Dharmawan Ronodipuro, an adviser to Security Minister Djoko Suyanto, says the government must use the resourcefulness that has led to the arrest of hundreds of suspected extremists over the past few years to tackle the spread of smaller cells. But, he cautions, the antiterrorism agency must focus on more than detention.
“We have to always maintain vigilance, because they are flexible people, they have imaginations, they readjust their system of what they’re doing. It doesn’t mean anything to just arrest somebody.”
While many see the weakening of JI as a positive thing, Mr. Ronodipuro worries that the country’s radical groups have merely broadened their operations. He and others note that extremist networks survive by blending the old ideology of creating an Islamic state with a new agenda, which is to be part of a global network of Al Qaeda.
The government is looking to tackle this new mode of terrorism through the upstart National Antiterrorism Agency and prevention campaigns that reach out to youth through tolerance-promoting comics and theater. Meanwhile, ad hoc programs aim to deradicalize convicted former terrorists by providing them with economic support for business start-ups.
But Ms. Jones of the International Crisis Group says that rather than targeting youths, the government should focus on the areas that have a history of extremist activity. She also notes that authorities should rein in state institutions, such as Islamic student organizations, that she says have been captured by hard-liners.
By failing to adequately address religious-based violence, which appears to be rising, the government may be undermining counterterrorism efforts, says Bonar Tigor Naipospos, head of the Setara Institute, a human rights monitor.