The Indonesians also received welcome help from abroad. The capture of al Qaeda leaders like Khalid Shaikh Mohammed and others in Pakistan helped to sever the key personal links between JI and al Qaeda's top leadership. Publicly, Bashir has always denied any links to al Qaeda, even while expressing support for bin Laden. "While al Qaeda and JI have similar ideologies," says one American counterterrorism official, "JI's leadership appears to understand that a formal alliance would elicit even more pressure from the Indonesian government."
The remnants of JI have largely split into two factions since 2005. The first is a smaller group of primarily younger die-hards and a few first-generation leaders. More willing to accept the collateral deaths of Muslims, this is the group most likely to pursue spectacular, al Qaeda-style attacks. The second and far larger group sees localized violence as necessary only on occasion. Officials say this group, having concluded that terrorist operations bring unacceptable levels of police attention, has basically returned to recruiting, political, and educational activities.
Fringe players. Jemaah Islamiyah could bounce back under the right leader. "JI has experienced some setbacks but is resilient," says a senior U.S. counterterrorism official. "JI has been able to regenerate leaders after such arrests are made." Indonesia's success has also created a new problem: Leaders like Bashir are losing their ability to rein in the most radical cells. The disorganization makes it even more difficult for security forces to track fringe players who might still be able to pull off small-scale attacks.
Over the past few years, the government has staged very public, prompt terrorism trials that have been closely watched by a citizenry unaccustomed to such transparency. Western intelligence officials credit the trials with helping to persuade many in Indonesia, which has a mostly moderate and secular Muslim population, that their country was facing a serious domestic threat, not just carrying out an effort imposed from abroad.
Indonesian police also made progress with an informal program to co-opt or deradicalize captured militants, similar to a controversial effort in Saudi Arabia. The program, which ignores the most committed militants to focus on JI's less fanatical members, is remarkable for just how modest it is in scope and budget—and how easily some of the militants can be bought. "Deradicalization is probably a misnomer," says Jones. "It's about countering militancy and committing to renouncing violence through economic perks." Often, the incentives amount to little more than the police paying the travel expenses of prisoners' wives for conjugal visits or funding children's schooling or family trips to Mecca, in exchange for the men abandoning terrorism.
The deradicalization program, the Indonesians say, has helped, if only by taking the deadly edge off extremist rhetoric. That's because former radicals often become more credible voices with the extremist community than moderate clerics.
Critics charge that trying to reform terrorists may undermine the rule of law. They point to an episode in which one of the men convicted in the Bali bombings, Ali Imron, was spotted by reporters in 2004 at a Jakarta Starbucks with one of the senior Indonesian generals investigating the attacks. Imron had avoided the death penalty and received a life sentence instead by expressing regret at his trial and providing information about the group. Australian victims' families were livid, but the Starbucks incident provoked little outrage in Indonesia, a country that is "far less puritanical" about law and order than the West, as one senior U.S. intelligence official puts it.
Indonesian officials are hoping the voices of moderation prevail even as they push to punish some of the most unrepentant offenders. Three men convicted in 2003 for their role in the Bali bombings have been sentenced to death, but their executions have been delayed by legal maneuvering.