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When the World Trade Center towers collapsed on the fateful morning of Sept. 11, 2001, it set in motion events half a world away that would change the face of security in Indonesia.

At some point after that, somewhere in Southeast Asia members of the Al Qaeda-linked Jemaah Islamiyah became emboldened enough to pull off the attack that led to Indonesia being labelled a hotbed of terrorism.

Before 9/11, Indonesia paid very little attention to acts of terrorism, seeing attacks like the bombing of the Jakarta Stock Exchange building in 2000 and a series of bombings of churches across the country on Christmas Eve that year as nothing more than criminal acts.

But the 2002 Bali Bombing that killed 202 people, many of them foreign visitors, changed all that.

The following year, Indonesia enacted the Law on Terrorism and formed Densus 88, a special police unit dedicated to combatting terrorism.

“Without 9/11 there wouldn’t be the US-led global war against terrorism,” International Crisis Group researcher Sidney Jones told the Jakarta Globe. “So there was so much international support for Indonesia, particularly after the first Bali bombing.”

While the majority of police officers in Indonesia still rely on outdated firearms or rifles from local munitions company Pindad, Densus 88 was equipped with the latest technology and trained by instructors from the US special forces and Federal Bureau of Investigation in addition to being funded by the US Department of State’s anti-terrorism assistance program.

Over the next decade, the antiterror unit would arrest more than 600 terrorism suspects and kill some of Asia’s most wanted terrorists, including JI leaders Noordin M. Top in 2009, Azahari Husin in 2007 and Dulmatin in 2010.

Jones said the overwhelming success of Indonesia’s fight against terrorism had almost completely undermined JI’s regional terror network.

But JI was not the only group inspired by Al Qaeda. Before 9/11, Islamic militants in Indonesia were largely engaged in sectarian conflicts in Ambon, Maluku, and Poso, Central Sulawesi, with little attachment to global terrorism networks or causes.

“After 9/11, local groups tried to associate themselves with Al Qaeda, to learn from its success,” terrorism analyst Noor Huda Ismail said. “9/11 successfully inspired Indonesian militants and exposed them to Al Qaeda-style ideologies, in turn increasing the lethality of the network.”

Taufik Andrie, research director for the Institute for International Peace Building, said the Indonesian government should keep a close eye on movements that glorify Osama bin Laden.

“Bin Laden’s ideology is so widespread through the teachings of [JI founder] Abdullah Sungkar,” he said. “Younger generations of terrorists consider Bin Laden a patron and try to emulate Al Qaeda-style attacks even though they lack direct channels to funding and training.”

And the police force is now becoming the victim of its own success, with JI-inspired lone wolves plotting attacks against the police, seen by radical Muslims as murderers of Islamic holy warriors. In 2010, a police station in North Sumatra was sprayed with bullets, killing three officers.

Further, Indonesia’s war on terror has been hampered by what is largely seen as its weakest link — the country’s penal system.

According to the ICG, some radicals finish their sentences with an even greater commitment to deadly jihad. Of 120 people arrested and 25 killed in counterterrorism raids since February 2010, 26 had previously been imprisoned for acts of terror.

In 2009, psychologist Sarlito Wirawan Sarwono, was commissioned by the government to evaluate its de-radicalization program.

“It is failing because there is no conceptual guidance,” Sarlito told the Globe. “Police think their job is over once terrorists are handed over to prison officials. Prison officials think it is the Social Affairs Ministry’s job once they re-enter society. So whose job is it?”