It was supposed to be one of Indonesia’s many successes; it was one of the reasons why the country’s President, Susilo Bambang Yudhoyono, was re-elected so overwhelmingly this month. Seven years after the horror of the Bali bombings, and numerous smaller explosions and killings, Indonesia had put Islamic terrorism back in its box.

That hope lay smouldering in the mangled interiors of the Ritz-Carlton and Marriott hotels in Jakarta, where at least eight people died yesterday. It is too early to pronounce on the identity of those responsible. But many Indonesians will have drawn their own conclusion: that Jemaah Islamiyah, the shadowy South-East Asian al-Qaeda affiliate, which had dropped from view in the past four years, is back.

Ninety per cent of Indonesia’s 239 million people are Muslims, the largest Islamic population in the world. Compared with the more austere forms practised in the Middle East and Pakistan, Indonesian Islam is tolerant, inclusive and liberal — although a minority loathe the West and sympathise with al-Qaeda.

Jemaah Islamiyah emerged in 2002 when the governments of Singapore, Malaysia and the Philippines announced the arrest of Islamic radicals said to have been plotting bombs against US, British and Australian targets. JI, whose name means “Islamic gathering”, was described as a clandestine organisation with cells across South-East Asia.

Most of its members were Indonesians, many of them former students at an Islamic boarding school in the Indonesian city of Solo. Its headmaster and the man described as the mastermind of the organisation was Abu Bakar Bashir, a white-bearded cleric who spoke of his admiration for Osama bin Laden.

After the Bali bombings in October 2002, counter-terrorism agencies arrested suspected JI members. They included Riduan Isamuddin, known as Hambali, JI’s alleged operations director who was accused of planning the attacks.

In 2003, three men — Ali Amrozi bin Haji Nurhasyim, Ali Gufron and Imam Samudra — were sentenced to death for the Bali attacks. Their executions were repeatedly delayed, apparently because of reluctance by the Indonesian Government to kill men regarded as heroes by a small but vocal minority. They were eventually executed by firing squad last November.

In co-operation with foreign governments, especially the US, Indonesia improved its counter-terrorism operations and since 2005, when suicide bombers killed 20 people on Bali, there have been no significant acts of terrorism in Indonesia. But documents seized in a raid in 2007 suggested that the organisation was merely biding its time.

That year the International Crisis Group, a think-tank that reports on Jemaah Islamiyah, wrote: “JI retains a solid core that probably totals more than 900 members across Indonesia. It likely is not growing but it retains deep roots and a long-term vision of establishing an Islamic state.”

JI was said to be organised into cells of religious “study circles” with half a dozen members.

But JI’s members are not the only Muslims in South-East Asia to be furious with Western foreign policy and disaffected with their governments. In April, ten men were sent to prison for organising a jihadi group in Palembang, Sumatra. They were originally fundamentalists, with no connection to terrorism, who were inspired by a fugitive member of JI from Singapore.

In a country as large as Indonesia, there are probably thousands like them, any of whom could have been responsible for yesterday’s carnage.

Times Recommends

• Tehran cannot live up to its rhetoric
• The new unicycle that will ‘change the world’
• We cannot wish away Iran’s bomb