JI’s goal is to establish a Daulah Islamiah, an Islamic caliphate, stretching across Southeast Asia, incorporating Indonesia, Malaysia, Singapore, Thailand, Cambodia, Brunei, the Philippines and parts of northern Australia.

JI is run like al Qaeda, with many small cells operating across the region. The organisation is divided into four mantiqis, each of which is responsible for carrying out operations in different areas. The leader of each mantiqi, according to the confessions of Mohammed Nazir bin Abbas, a JI chief, reported to spiritual leader Bashir every six months, either directly or in writing. JI also has an economic wing, called the iqtisod, which finances its operations, travel for members to Afghanistan and other places for training, the purchase of explosives and also the JI-run madrassas (religious schools). JI has at least four front companies in Malaysia. JI also gets money from foreign charities, such as the Saudi group Al Haramain.

JI’s roots go back to Darul Islam (DI), an organisation formed in the 1940s in Indonesia that fought for an Islamic state in Indonesia. In the 1980s, many DI members, including Abu Bakar Bashir and Abdullah Sungkar, fled to Malaysia to avoid arrest by the Suharto regime. Bashir and Sungkar founded Jemaah Islamiah in the late 1980s. Sungkar went to Afghanistan to fight the Soviets, where he began fomenting a relationship with al-Qaeda. In 1993, he recrutied jihadists in Pakistan to join his new group, JI. The chairman of this faction, according to Nazir, was Osama bin Laden. Among the members were two of the Bali bombers. Sungkar also sent several JI members to train with al-Qaeda.

Meanwhile, al Qaeda began establishing its own connections in Southeast Asia. Osama bin Laden sent his brother-in-law Mohammed Jamal Khalifa, Khalid Sheikh Mohammed (head of al Qaeda’s military committee) and Ramzi Ahmed Yousef (who bombed the World Trade Centre in 1993) to the Philippines in 1988 to establish ties with the Moro Islamic Liberation Front (MILF). Khalifa set up charities in the southern Philippines, with much of the money raised used to purchase weapons and conduct operations. In addition to training the MILF, they developed Oplan Bojinka, a plan to assassinate the pope and then-US President Bill Clinton in Manila, and to blow up eleven aeroplanes over the Pacific in early 1995. The plan included hijacking planes and crashing them into the CIA, Pentagon and World Trade Centre. (This later became the blueprint for September 11). As a practice run, they exploded a bomb on a Philippines Airlines flight to Tokyo in December 1994. Oplan Bojinka never materialised because the chemicals to be used exploded prematurely.

JI stepped up its own operations in the region in the late 1990s. According to the confessions of Omar al-Faruq, a top al Qaeda operative in Southeast Asia captured in June 2002, Bashir is responsible for a bomb that exploded outside the largest mosque in Jakarta in 1999, at the time believed to be set off by Christians. Bashir’s intent was to increase tensions between the Muslims and Christians in Indonesia.

According to a CIA summary of Faruq’s September 2002 confession, he entered Indonesia in the late 1990s to take control of al Qaeda operations in the region. Bashir and Sungkar also returned to Indonesia after Suharto’s fall in 1998, sensing an opportunity to expand JI’s activities there. In mid-1999, Faruq engaged in a number of unsuccessful terrorist plots in Indonesia. In May, he met with several operatives to plan the assassination of Megawati Sukarnoputri, then a presidential candidate. They bought weapons in Malaysia and the Philippines but were unable to get them into Indonesia . Further links between al Qaeda and JI were confirmed in 2001 when a tape recorded in Singapore in 1999 was found in Afghanistan in the home of al-Qaeda operations chief Mohamed Atef. In the video, Singapore JI member Khalid Jaffar told of plans to attack US interests in Singapore and included surveillance of the Yishun Mass Rapid Transport station, frequented by US military personnel. After viewing the video, al Qaeda leaders instructed JI to procure explosives and recruit men for the attack. For unknown reasons, the attack never occurred.

By 2000, al Qaeda and JI were closely linked. In January 2000, JI operations chief Hambali hosted a meeting in a building owned by JI member Yazid Sufaat in Kuala Lumpur that many al Qaeda operatives attended, including Khalid Sheikh Mohammed and Khalid al-Mihdhar and Nawaf al-Hamzi, both of whom were among the hijackers of the plane that hit the Pentagon on September 11, 2001; and another operative accused of the 2000 attack on the USS Cole. Also in Malaysia in 2000, according to an intelligence report, a high-ranking JI member hosted Zacarias Moussaoui, the "twentieth hijacker," who told him to buy four tons of fertiliser to build a bomb.

Meanwhile, JI continued to develop. Abdullah Sungkar died in 1999, leaving Bashir as the sole spiritual leader. His counterpart is the group’s master strategist and operations chief Riduan Isamuddin, known as Hambali. Hambali lived in Malaysia from 1985-87, then went to Pakistan, fought in Afghanistan and joined al-Qaeda. Upon his return to Southeast Asia, he was instrumental in building up the al-Qaeda/JI network. In 1999 Hambali instructed all JI groups to convert into operational cells and to send as many men as possible to Afghanistan or Mindanao for training. In 1997, the MILF had permitted JI to set up their own terrorist training camp within Camp Abu Bakar in the Philippines.

Also at this time Bashir initiated a regional alliance of jihad groups, the Rabitatul Mujahidin (Mujahidin Coalition). The purpose was for the member groups to cooperate and share resources for training, purchasing arms and carrying out operations in order to form an Islamic state. The coalition met three times in 1999 and 2000 in Malaysia. At one of the meetings, a resolution was passed to attack Philippine interests in Indonesia. In August 2000 a bomb exploded outside the Philippines’ ambassador’s house in Jakarta. Intelligence links this attack to Hambali and claims that it was sanctioned and coordinated by the coalition.

At another meeting of the Rabitatul Mujahidin, plans were made to bomb churches in Indonesia, target Western interests and attack the US. In one of JI’s biggest operations thus far, simultaneous explosions ripped through 17 churches across Indonesia on Christmas Eve 2000. A CIA report labels Faruq as the "mastermind" behind these bombings.

On December 30, JI was responsible for the attack that hit five targets in Manila, killing another twenty-two. Indonesian JI member Fathur Rohman al-Ghozi captured in January 2002 confirmed that the bombings had been coordinated and funded by Hambali.

In May 2001, Faruq, on orders from al Qaeda operative Abu Zubaydah, planned an attack similar to the bombing of the USS Cole in Yemen, this time on a US naval ship in the Surabaya harbour in Indonesia. The attack on the ship never occurred because Faruq was unable to recruit enough people to carry it out. In August, Faruq attempted for the second time to assassinate Megawati. He drew up plans to explode a bomb at a meeting of Megawati and other Indonesian leaders. This attempt failed when the bomb exploded prematurely near the Atrium mall in Jakarta.

The next major attack was planned for December 2001 in Singapore. In Operation Jibril, the American, Israeli and Australian embassies, as well as American ships in Singapore’s harbour, were targeted. The intent was for trucks loaded with explosives to blow up outside each target.

The groundwork for the attack began in 1993, when the Singapore branch was formed by Ibrahim Maidin under the direction of Hambali who was then operating from Kuala Lumpur. The first Singapore cell became operational in 1997 and the second in 2001. Members were aided by al-Qaeda experts known as Mike and Sammy, later revealed to be explosive experts al-Ghozi and Jabarah Mohammed Mansour, a Canadian al Qaeda member of Kuwaiti descent. The cell members were to scout out the targets, videotape them, arrange travel documents and procure explosives. Yazid Sufaat, a US-trained biochemist with a front company in Kuala Lumpur, was ordered to buy twenty tons of ammonium nitrate fertiliser. Then suicide bombers would be brought in and members of the cell would slip away.

However, before the plan could be carried out, Singapore authorities arrested thirteen JI members. Singapore’s security agency, the ISD, had become suspicious when a local company alerted them about a large order of ammonium nitrate. A month later, al-Ghozi was arrested. In April 2002 he was sentenced to twelve years in jail in the Philippines, but he escaped last month. Authorities also found explosives and rifles hidden in the southern Philippines that were to have been used in the attacks (more explosives to be used in the attack were not discovered until March 2003, in Johor, Malaysia). Indonesian officials reported finding a document called "Jihad Operation in Asia," which detailed plans to bomb American embassies in Singapore, Kuala Lumpur, and Jakarta. The ISD arrested another seventeen JI members in August 2002.

The arrests may have stopped the planned attacks in Singapore, but they did not deter other JI members from meeting to plot more attacks. In January 2002, JI met in southern Thailand to plan the next big operation. Hambali attended this meeting. In February, Bashir met with six JI officials in Bangkok, where he reportedly declared that Australia would be destroyed if it continued to talk about pre-emptive strikes in the region. At this meeting, Bali was chosen as a potential location for a future attack. Shortly thereafter, money for the attack was transferred between JI operatives.

By September, regional and Western governments sensed that an attack was being planned, mostly fearing attacks against US interests to commemorate the anniversary of September 11. Faruq confessed that JI was prepared to conduct simultaneous car/truck bomb attacks at US embassies in the region on or around September 11.

On October 12, 2002, JI carried out the terrorist attack in Bali, exploding two bombs that killed 202 people. Recent confessions by JI members placed on trial for this attack confirm that Bali was chosen in order to target Westerners.

After Bali, JI is believed to have carried out several smaller attacks. A small bomb exploded on October 24 in a mall in Bandung in Indonesia. In December, two bombs exploded in Makassar. The same bombers were responsible for an explosion there in 2001 and planned to bomb churches in Makassar and South Sulawesi. In February, a small bomb exploded at the national police headquarters in Jakarta. Meanwhile back in October in Thailand, five schools were torched and two bombs exploded (a third was defused). Officials originally denied that the attacks were related to JI, but it was later discovered that the bombers had been in contact with al Qaeda during the year before the attack.

JI has a presence in Australia as well, numbering around one hundred members, according to "The Australian Connections", a program aired on Four Corners on 9 June 2003. While Bashir and Sungkar were in Malaysia, they turned their attention to Australia, and appointed Abdul Rahim Ayub, an Indonesian follower, to lead the new JI branch in the early 1990s. Abdul Rahim is still believed to be the head of Mantiqi 4, though he left Australia last September. Initially, the role of this branch was to raise funds. However, Abdul Rahim was in contact with Hambali, who began recruiting Australians for operations. Hambali planned attacks on the Sydney Olympics in 2000, and went as far as recruiting operatives and training them. However, for reasons still unknown, Abdul Rahim rejected the plans. Following the Bali attacks, ASIO raided several homes in Sydney, Melbourne and Perth, confirming JI’s presence, which they had been tracking for a year. Combat training camps were discovered in a remote forest outside Melbourne. An article in The Age on 14 July reported that police also revealed that a network of Australians continues to give financial and logistical support to terrorists overseas.

Just days after the Bali attack, Australia called for JI to be listed as a terrorist organisation by the UN. On October 27, the UN put JI on the terrorist list. Malaysia, Indonesia, the Philippines, Thailand and Cambodia signed an agreement to cooperate on exchanging information and establishing communication about terrorist threats.

Meanwhile, Indonesia immediately instituted new emergency powers to deal with terrorists, which permits detaining suspects for almost a year without trial and seeking the death penalty for convicted terrorists. Indonesian authorities arrested Bashir, whom they had let go after light questioning in February. He was not arrested on charges relating to the Bali attack in particular, but for many of the attacks for which Faruq named him responsible, including the Christmas Eve bombings in 2000. Bashir’s trial for treason began in April.

After a few months of relative quiet, new developments in the JI case began in April. Eighteen JI members, including Bashir’s successor Abu Rusdan who in May admitted his role in planning a series of bombings in Indonesia and the Philippines, were arrested in Indonesia. Intelligence revealed that at least sixteen JI members, including Rahim Ayub, met in Indonesia in April. The June arrest of Idris, one of the key financiers of the Bali attack, revealed that he had been travelling around the region meeting with JI members and was in the process of planning another attack with money he had stolen from a bank in Sumatra.

In recent months, even Thailand has joined the effort to fight terrorism in the region. Though the Thai government in the past denied any terrorist presence in the country, in May PM Thaskin Shinawarta conceded that JI does have members in Thailand. This statement followed the arrests of two Thais in Cambodia for being members of JI. In June, Thai police arrested three suspected JI members in Bangkok. Reports claim that they had planned to attack the Singaporean, Australian, American, Israeli and British embassies in Bangkok, as well as two beach resorts. In July, a Thai explosives expert, Samarn Wae-ajl, surrendered himself and admitted that the attacks were scheduled for the APEC summit in October, to be attended by Howard and Bush.

Arrests continued in Indonesia this month, with police catching nine JI members and finding explosives and evidence that led them to believe the group was planning attacks on churches and shopping malls and the assassination of public figures. Yet experts point out that over 500 JI members have attended training camps over the past two decades, and only 140 of them have been caught. A small explosion, potentially the work of JI, at Indonesia’s Parliament building on July 14 and al-Ghozi’s recent escape show that despite the arrests, the threat of JI and militant Islam in the region is still very real.