Another alleged Bali bombings mastermind, Dulmatin, was shot to death in a raid. Radical Muslim cleric Abu Bakar Bashir was arrested; last year he was sentenced to 15 years in jail.
That led Indonesian extremist religious leaders to order militants to change their mission. Instead of going after Westerners and American symbols they were directed to target Indonesian 'infidels' such as police, anti-terrorism squads, lawmakers and others deemed as obstacles to transforming the secular country into an Islamic state governed by Sharia law.
Most of Indonesia, a country of 240 million, practices a moderate style of Islam that condemns violence, and its government is keeping up pressure against extremists. Data from the National Police revealed more than 700 militants have been arrested over the past 10 years, including 84 last year. Dozens more have been killed since the Bali bombings.
Though the number of domestic terrorist attacks has risen, suicide bombers are more likely to act alone or in smaller groups than they did in years past.
"I don't think there is any one person who is the current face of terrorism in Indonesia," said Ken Conboy, a Jakarta-based expert on Southeast Asian terrorism. "Rather, the terrorists have splintered into small cells that have only fleeting contact, if that, with one another."
That lack of organization makes it more difficult to pull off devastating attacks.
Last year, a suicide bomber blew himself up inside a mosque packed with police, injuring 30 people, and another detonated his explosives in a church in Central Java's Solo town, dying instantly and wounding 22 worshippers.
Just last month, police arrested 10 Islamist militants and seized a dozen homemade bombs from a group suspected of planning suicide attacks against security forces and plotting to blow up the parliament building. The alleged bomb maker, Muhammad Toriq, turned himself in to police while wearing an empty suicide vest.
The explosives seized were pipe bombs, dangerous but much less powerful than those used in Bali 10 years ago. But other would-be suicide bombers remain at large.
In March, authorities received an intelligence tip that at least one jihadist "groom" had arrived in Bali. They found a note he wrote to his family, saying he would carry out a suicide mission with God's blessing and that the family would be reunited in paradise, said Ansyaad Mbai, who heads the country's anti-terrorism agency.
Security forces killed five suspects who were believed to be plotting several armed robberies in Bali to fund their terrorist activities. But the groom got away, and it's unclear what attack he had planned or whether he will still attempt it.