JOINT SPECIAL OPERATIONS FORCES SENIOR ENLISTED ACADEMY 

A COUNTERTERRORISM ANALYSIS 

THE BALI PARADOX 

AN EXAMINATION OF JEMAAH ISLAMIYAH 1992-2002 

BY 

 GREG SMITH 

APRIL 2011 

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The Bali Paradox: An Examination of Jemaah Islamiyah 1992-2002

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Smith, Gregory

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Joint Special Operations University,7701 Tampa Point

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14. ABSTRACT

Counterterrorism (CT) policy is like a game of chess. It often evolves as the result of a terrorist act or

campaign. The objective of an effective CT policy is to identify and address the conditions that lead a

terrorist group to act. It requires all facets of political, military, intelligence, and law enforcement planning

to identify the root causes before a common thread binds these causes into a definable terrorist group. The

history of Indonesia is defined by struggle: the struggle for independence from Dutch colonial rule, the

struggle to establish the Islamic State of Indonesia, the struggle for self determination by the people of

Indonesia from an authoritarian regime. These all play significant roles in the psyche of the population.

15. SUBJECT TERMS

Counterterrorism, Irregular Warfare

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Standard Form 298 (Rev. 8-98)

Prescribed by ANSI Std Z39-18 
PREFACE 

Counterterrorism (CT) policy is like a game of chess. It often evolves as the result of a terrorist 

act or campaign. The objective of an effective CT policy is to identify and address the 

conditions that lead a terrorist group to act. It requires all facets of political, military, 

intelligence, and law enforcement planning to identify the root causes before a common thread 

binds these causes into a definable terrorist group. The history of Indonesia is defined by 

struggle: the struggle for independence from Dutch colonial rule, the struggle to establish the 

Islamic State of Indonesia, the struggle for self determination by the people of Indonesia from an 

authoritarian regime. These all play significant roles in the psyche of the population. 

This paper is simply an academic analysis of the strategic and operational environment in 

Indonesia prior to the Bali bombings. It is organized into five chapters that focus on the terrorist 

group Jemaah Islamiyah (JI). The overall intent of the first chapter is twofold. First, it aims to 

academically examine the origins of JI in terms of the antecedent conditions that, collectively, 

led to its creation and decision to conduct terrorist activities. Second, it hopes to identify the 

actors that helped to bond the antecedents together. 

The second chapter examines the series of events that occur once the antecedents are fused into 

Jemaah Islamiyah. The focus of this chapter is the emergence of sub-actors that occurs as a 

2 
result of recruitment. Additionally, the evolution from thought and rhetoric to a decision to act is 

often the result of a reinforcement of ideology that comes from organization. A highly organized 

structure will promote and maintain the goal of its leader and communicate across lines 

effectively. Without barriers, the organization will flourish. 

The third chapter will primarily focus on the Christmas Eve church bombings of 2000. The 

intricate details of execution are often the result of the person planning the event. The more 

experienced the person is in planning, the higher probability of success. 

The fourth chapter will examine Jemaah Islamiyah from an academic perspective. Did the group 

meet the criteria of a terrorist organization prior to the attacks on Christmas Eve 2000? 

Additional focus is placed on the role of religion and societal conditions that steer a group to 

commit terrorist acts. Finally, there is an examination of the new terrorist model as it pertains to 

Jemaah Islamiyah’s development. 

The fifth and final chapter will evaluate Indonesia’s political history and the effect the highly 

centralized government of Suharto had on the evolution of militant Islamic movements in 

Indonesia. Attention will be given to the fractured political structure following Suharto’s 

downfall and the emergence of a decentralized political infrastructure. This paper will conclude 

with the future of Indonesia’s CT strategy and how its continual evolution is essential to break 

the Bali Paradox. 

Several key non-state actors and events are deliberately omitted from this paper. These actors 

either did not come to center stage until after the Christmas Eve church bombings or do not add 

to the main points specifically addressed in this paper. Events not mentioned, while important to 

the overall history of Indonesia and conflict, were not required to reinforce the overall objective 

of this paper. 

3 
CHAPTER ONE: ORIGINS OF A CONFLICT: WHO IS JEMAAH ISLAMIYAH? 

INTRODUCTION 

To know your enemy, you must know yourself. This quip is often used but rarely practiced. The 

culture of the United States is “instant” everything. From coffee and breakfast in the morning to 

dinner at night, everything either comes out of a window or out of the microwave. As a culture, 

we are conditioned to apply these norms to all facets of life. When it comes to intelligence and 

counterterrorism, we often want the situation reports now. We attempt to establish policy and 

then immediately put a mechanism in motion in order to assess it, adjust fire, and re-implement. 

The problem with this concept is the relevant actors to our script do not think this way. They 

behave and adopt their policies amidst societal norms that entirely contradict ours. This said, in 

intelligence and counterterrorism, many times our greatest enemy is ourselves. 

This chapter examines the history of the terrorist group Jemaah Islamiyah (JI). Particular focus is 

placed on the origin and organizational structure of JI as well as the events that led to its 

creation. 

4 
ORIGINS 

The emergence of militant Islam began with the Darul Islam (DI) movement in 19481. It 

actually began as several separate rebellions that morphed into a common cause. The 

overarching goal of DI was originally to establish an Islamic State in Indonesia. Particularly 

germane to our discussion is how DI survived over these many years 

and how it serves as a model to JI and other militant movements in 

Southeast Asia. DI’s rebellion was primarily inspired by 

dissatisfaction amongst the local militias regarding concessions 

made by the newly created Indonesian government to the Dutch 

former colonial power2

. DI eventually consolidated its several 

factions and merged them into the Negara Islam Indonesia (Islamic 

state of Indonesia) (NII) rebellion. 

 

The rebellion lasted thirteen years and cost nearly 20,000 lives3

. The rise of communism and the 

Sukarno regime ushered in a new struggle for DI. The original rebellion was defeated by the 

Indonesian military in 1962. Its founder was executed and the movement was left with a power 

vacuum. DI underwent significant organizational changes in the ensuing struggle for control. In 

1965, the DI and the United States backed Major General Suharto during a military coup. As 

Suharto took control, he reversed the previous course of events and denied DI and all other 

Muslim organizations a seat at the political table4

. Suharto viewed the Islamic movements in 

Indonesia as a threat to national power and sought to curb their influence. The Suharto regime 

forced DI to consolidate its position and develop a new strategy for the future. The most 

important aspect of the DI movement is its resilience. Its ability to withstand significant loss and 

still maintain some form of command and control and strategic outlook serves as a model for 

militant movements today. 

ABDULLAH SUNGKAR 

Abdullah Sungkar was a Muslim cleric that left the NII movement and founded Jemaah 

Islamiyah in 1993. A significant rift had developed within NII and Sungkar 

opted to leave5. He was born in 1937 and was of Hadrami descent6. Sungkar 

was a veteran of the Islamic youth and political movement in Indonesia. 

Abdullah Sungkar was of the hard line Wahhabi sect of Islam. He was the 

ideological heir of Kartosuwirjo, the original founder of Darul Islam7

. 

Sungkar was motivated by the idea that Islam should be the only religion with 

Sharia as its only law and any attempt to subjugate Islam was blasphemy and 

should be fought. Islamic governments throughout the Middle East such as 

Saudi Arabia supported the movement though Islamic charity organizations 

and financial assistance8

. 

1

 International Crisis Group; “Recycling Militants in Indonesia”; 22 February 2005 

2

 ibid 

3

 Ismail, Noor. “Schooled for a house of Islam” 25 August 2005. www.yaleglobal.org 

4

 Abuza, Zachary. “Muslims, Violence, and Politics in Indonesia” 3 September 2004. www.nbr.org 5

 Eliroz, Giora. “Islam and Polity in Indonesia” 1 February 2007. www.hudson.org 6

 The Hadrami tribe is of Yemeni origin. Early Islamic merchants from Yemen came to Indonesia in the 15th

century. Bin Laden’s family is also originally from Yemen. This is important when the examining the link to AQ. 

7

 Abuza, Zachary. “The War on Terrorism in Southeast Asia”, Strategic Asia 2003-2004. www.nbr.org 8

 Bubalo, Anthony and Fealy, Greg; “Between the Global and the Local; Islamism, the Middle East, and Indonesia” 

October 2005. The Brookings Project on U.S. Policy Toward the Islamic World 

5 
ABU BAKAR BASHIR 

Abu Bakar Bashir is probably the most famous member of JI. He was born in 1938 and is also 

Hadrami. While he was not part of the original DI movement, Bashir was very active in the 

1950s with Muslim youth networks. This is where he came to know 

Abdullah Sungkar. Throughout the 1960s, Bashir became more 

radicalized and, together with Abdullah Sungkar, founded the Radio 

Dakwah Islamiyah Surakarta. While Sungkar was violently antiChristian in nature, Bashir chose a more political path and often 

strategically considered his next steps. Bashir was violently anti-Western 

and anti-Christian, but he weighed the consequences of action versus 

rhetoric. Bashir used rhetoric and his Islamic schools as recruiting tools 

but also evaluated the political process in Indonesia and looked for ways 

to promote Sharia law and Islam through the means other than terrorism. 

 

Sungkar and Bashir operated the Radio Dakwah Islamiyah Surakarta for four years and then 

moved their operation to the village of Ngruki on the island of Solo. In 1973, this movement 

became the Pondok Ngruki9.

RADICALIZATION 

Pondok Ngruki is a religious boarding school on Solo Island, Indonesia. The school is 

noteworthy because it serves as the single source for every Indonesian militant with suspected 

ties to Al Qaeda10. The school began to develop throughout the mid to late 1970s until Sungkar 

and Bashir were arrested for trying to form a militant organization. Both men were sentenced to 

nine years in prison for subversion. The sentences were reduced to just short of four years. 

Sungkar and Bashir were freed from prison in 1983 and fled to Malaysia in 1985. While in 

Malaysia, Sungkar and Bashir were neighbors with Fauzi Hasbi, a Free Aceh Movement (GAM) 

defector with ties to both GAM and the Indonesian Special Forces unit Kopassus11. Several 

incidents occurred during and after the imprisonment of Sungkar and Bashir that signified a 

violent shift from theory to operation. 

Immediately after Sungkar and Bashir were imprisoned, there was a spike in violent crime that 

can be attributed to Pondok Ngruki. A murder and several attempted robberies signified the first 

instance of societal crime for the purpose of Islamic fundraising12. These crimes were 

committed both to demonstrate displeasure with the Indonesian 

government’s actions and to raise funding for Sungkar and 

Bashir. Additionally, the political climate was beginning to shift 

and the Usroh13activists in central Java were becoming more 

energized. The climate in Indonesia throughout the 1980s was 

moving toward the radical end of the continuum at an alarming 

rate. 

9

 International Crisis Group; “Al Qaeda in Southeast Asia; The Ngruki Group” 8 August 2002 10 ibid 

11 International Crisis Group; “How the Jemaah Islamiyah Terrorist Network Operates” 11 December 2002 12 International Crisis Group; “Al Qaeda in Southeast Asia; The Ngruki Group” 8 August 2002 13 Human Rights Watch; “Indonesia’s Prisoners”; June 1998. www.hrw.org 

6 
By 1990, there were more than seven different active Islamic movements. With potential 

flashpoints at Aceh, Moluccas, Solo and Java, the conditions ripened for extremist ideology to 

flourish. The strict control of the Suharto regime kept all parties from action. With Sungkar and 

Bashir both living in Malaysia, they were openly preaching ideologies that paved the way for 

future events. 

THE FOUNDING OF JEMAAH ISLAMIYAH 

When the Soviet Union invaded Afghanistan in 1979, no one could have possibly predicted the 

amount of support, financing, and fighters the mujahedin resistance would receive over the next 

nine years. Nearly every Muslim in the world felt a duty to defy tyranny and invasion by any 

means available. For Indonesians already immersed in the Islamic struggle narrative from the 

DI/NII movement and radicalized by Pondok Ngruki and Usroh ideas, the opportunity to go and 

fight in Afghanistan was simply too tempting to let pass by. 

In the wake of the collapse of the Soviet Union, the idea of an Islamic Caliphate resurfaced. 

Indonesia was never part of the original idea of the Caliphate. However, as the country with the 

world’s largest Muslim population, Indonesia gained 

strategic importance as a result of its recruitment base and 

strategic location. Indonesia lies along the Straits of 

Malacca, serving as a vital transit point for trade and travel. 

Following the Afghan campaign, many fighters returned to 

Indonesia and throughout Southeast Asia battle hardened 

and unafraid of further conflict14. Islamic leaders were 

quick to recognize the strategic importance of Indonesia to 

the world. With tensions boiling over in the Philippines, 

Indonesia was quickly absorbed into the vision of a new 

Global Islamic Caliphate. The Islamic world had defeated 

the Soviet Union in Afghanistan. They had proven they were capable of triumphing over 

oppression through Jihad. The loss of a “two-sided” conflict gave way to a shared animosity 

toward the new perceived oppressors, the United States and the West. 

Significant internal arguments within both the DI and GAM movements had also occurred 

around the same time. Many members in exile in Sweden15 argued over ideology and the way 

ahead for both groups. JI founders Bashir and Sungkar saw this as the right time to enact a new 

vision. 

Bashir and Sungkar created JI on 1 January 1993 and published the General Guide for the 

Struggle of Al Jama’ah Al-Islamiyah (PUPJI)16. This was a significant advance from previous 

movements as it had a clearly defined organizational structure and a strategic outcome measured 

 

14 PBS video “The Al Qaeda Files” discusses the post Afghan conflict and the foreign fighters. Several ICG reports 

discuss JI members fighting in Afghanistan. 

15 Hasan di Toro and Abu Hasbi Geudong (Fauzi’s father who died in 1993) were in Sweden arguing over GAM 

future while GAM fighters were still active in Aceh. Di Toro would have a stroke in 1999 and GAM would split 

into two over a power struggle between di Toro and Haseini (the chief of staff of GAM). The result was GAM and 

MP-GAM. This debate also spilled into the Philippines where ASG and MILF commanders argued over the way 

ahead. The result was a lot of fighters moving between groups across SE Asia. Omar al-Faruq would arrive in 1999 

to organize JI along AQ lines of operation. 

16 Pavlova, Elena. “From Counter-Society to Counter-State; JI according to PUPJI”; 14 November 2006; Singapore 

Institute of Defence and Strategic Studies. 

7 
over three definable phases: Faith’s Strength, Brotherhood’s Strength, and Military Strength17. 

From 1993-1996, Sungkar served as the emir of JI and its spiritual leader. He had always been 

the political mind of JI with Bashir promoting the group’s anti-Western and militant views. 

Source: CIA maps. Overlay drawn by Smith on PowerPoint and saved as picture 

From JI’s inception, it was subdivided in a highly organized structure. The regions were divided 

into four Mantiqis or territories. Similar to a military organization, each Mantiqi reports to the 

overall JI leadership. 

Source: dfat.gov.au/JI structure/ch4

 

17 Ibid. pg 12 

8 
Under each Mantiqi is a Wakalah18 (district,) followed by Kirdas (sectors) and finally a Fiah or 

individual cell. This highly developed order of battle is strikingly similar to most military 

organizations. One can infer that JI was established with militaristic objectives to achieve an 

operational effect furthering the strategic vision of a pan-Islamic Caliphate. 

THE CAMPAIGN: ENTER HAMBALI 

With the establishment of JI as an operational entity, JI simply needed to find a tactician to take 

the Jihad concept from ideology to reality. Sungkar and Bashir found that man in Riduam 

Isamuddin, known by the international community as Hambali19. He took his name after Imam 

Hambal, a religious leader (780-855A.D.) and founder of the Hambal school of Fiqh20. Imam 

Hambal is regarded as the 13th Imam of Islam and is founder of one of the four schools of 

Islamic religious law. Hambali lived with Sungkar and 

Bashir in Malaysia in the early 1990s. He went on to serve 

as a key member of the Konsojaya import-export company. 

Little was known of him until his Konsojaya Company 

surfaced in connection with a terrorist plot to plant bombs 

on several airliners. This plot was called “Operation 

Bojinka”21. Bojinka was masterminded by the renowned 

terrorist Khalid Sheikh Mohammed and World Trade 

Center bomber Ramzi Yousef. The fact that Hambali was not arrested following this event set 

into motion a chain of events that would change the face of terrorism in Indonesia in the coming 

years. Hambali was militaristic in nature and would prove to be an elusive target in the years to 

come. 

 The Asian financial crisis of 1997-1998 resulted in political turmoil across Indonesia. Student 

protests and mass demonstrations forced Suharto to relinquish 

power. With his exit, three decades of control of the Islamic 

movement had come to an end. In 1999, Abdullah Sungkar died 

of cancer. This left Abu Bakar Bashir as the spiritual leader and 

emir of Jemaah Islamiyah. Bashir quickly consolidated power 

and prepared to move JI forward. The timing between Sungkar’s 

death, Suharto’s fall, Al Qaeda’s declaration of war against the 

US, and JI’s rise to power are highly interrelated. Bashir 

returned to Indonesia and prepared for the next phase. JI began a masterful campaign of anti-US 

and anti-Western rhetoric and used conflicts in the Moluccas, East Timor, and the Muslim 

offensive in the Philippines as a catalyst to move forward. Hambali began significant 

coordination with key Al Qaeda figures and JI declared allegiance to the Al Qaeda organization. 

JI used this time to cement relationships with groups such as Abu Sayyaf and the Moro Islamic 

Liberation Front in the Philippines22 as well as local groups such as the revived Darul Islam 

movement, Laskar Jiha 23 d, and Kompak . 

 

18 A Wakalah is also called a Sariyah. In some Jihadist groups it is similar to a battalion or brigade. 

19 Hambali was known as the Osama bin Laden of Southeast Asia 

20 See “The 100 Great Muslims” http://www.renaissance.com.pk/mjuletfor96.html It is important to note that the 

Hambal region includes all of Saudi Arabia. The Wahhabi movement is closely linked to the Hambal School. 

Based on this analysis, Hambali would likely have the same ideological background as AQ members. 

21 http://en.wikipedia.org/wiki/Hambali 

22 The MILF is an Islamic separatist group in the Philippines. Abu Sayyaf is an offshoot of this group and the 

MNLF. ASG’s leader Janjalani fought along side the Taliban, Hambali, and other JI members in Afghanistan. 

9 
In January 2000, several high ranking Al Qaeda members, along with members of JI and other 

groups attended a meeting in Kuala Lumpur, Malaysia24. The Malaysian authorities took 

pictures of this meeting but no audio recordings were made. For JI, Hambali and a man named 

Yazid Sufaat25 attended. Sufaat had attended school in the United States and had obtained a 

degree in biochemistry. He had also spent time in the Malaysian army. Sufaat had been a loyal 

member of JI since its inception in 199326. Based on the widespread attendance, it could have 

appeared the world was on the verge of a global jihad. 

 Source: http://www.tkb.org/ (overlay done by Smith for graphic purposes) 

OVERVIEW OF SOUTHEAST ASIA – AL QAEDA NEXUS 

CONCLUSION 

Every potential enemy is a puzzle to intelligence and counterterrorism officers. It is much easier 

to took at history and see what is obvious. An understanding of the present and the future 

continues to prove much more elusive than an understanding of the past. With Bashir and 

Hambali in close coordination with AQ, the timing was right to launch an offensive. With bin 

Laden’s Fatwa and the increasing momentum of this new global jihadist network, JI had to 

transition to action. Their next difficult tasks would be selecting the appropriate target set and 

continuing to develop, recruit, train, and prepare. It proved be a task JI was equipped to 

accomplish. 

 When he returned home, he broke away from the MNLF and began a campaign of hostage taking presumably to 

secure funding. Both groups provide training and logistical bases to members of JI. JI enjoys a logistical and, at 

times, C2 relationship with these groups. 

23 Government of Australia; “Report of JI Activities” 5 May 2003. Attach B pg. 2 

24 http://en.wikipedia.org/wiki/2000_Al_Qaeda_Summit 

25 http://en.wikipedia.org/wiki/Yazid_Sufaat 

26 Yazid Sufaat will be discussed in the coming chapters so he is important to note as present at this high level 

meeting in Kuala Lumpur. 

10 
CHAPTER TWO: GOING OPERATIONAL; DEVISING THE PLAN 

Source: caosblog.com

INTRODUCTION 

Hindsight is 20/20 vision. It is easy to say that you should have noticed this or you would have 

noticed that. The fact remains counterterrorism efforts have failed once the terrorist act occurs. 

This is what makes this topic so debatable, so nebulous, and so controversial. When dealing 

with extremist groups, it is difficult to discern between action provoking messages and political 

rhetoric. One thing is certain, most extremist groups follow a campaign that evolves with the 

political climate associated with the movement. 

This chapter will discuss the events that led to the Christmas Eve church bombings that occurred 

across Indonesia in 2000. The focus will be the key participants and the political objective of the 

attack. Finally, we will examine Indonesia’s security apparatus at the time of the attacks and set 

the stage for the Jemaah Islamiyah’s first “spectacular.” 

11 
JEMAAH ISLAMIYAH; RISE TO POWER 

As mentioned in chapter one, there were several significant events that contributed to JI’s rise to 

power in the late 1990s. The fall of the Suharto regime significantly aided in the development 

and radicalization of JI. For thirty years, Suharto’s New Order policy27 carefully balanced 

competing interests and established a hierarchal, highly centralized government with little room 

for political debate. Islamic movements were suppressed from engaging in significant antigovernment rhetoric for fear of repression. Suharto’s tight control over his regime also created 

internal disagreements between the Indonesian Intelligence Organization Bakan28 and the 

Indonesian police agencies. This lack of communication offered JI members the time to 

coordinate their next move without interference. 

When Suharto resigned from power in 1998, it left a political void in Indonesia. The 

authoritarian rule that had become ingrained in everyday Indonesian life was replaced by a 

significantly more decentralized government. The military 

and security services would devolve and have to relinquish 

power. Sungkar and Bashir, having already established a 

thriving JI school in Malaysia, returned to Indonesia and their 

school at Pondok Ngruki29. What is most important to note 

is that the political landscape had changed across Indonesia. 

With democracy in a fledgling state, it was now politically 

acceptable to openly campaign for reforms. Some Muslim 

leaders used this time to pressure the government to establish dialogue and concessions. Others, 

such as Sungkar and Bashir, wanted the establishment of an Islamic State and Sharia law30. 

In 1999, Abdullah Sungkar died31. Before he died he had developed an almost fanatical 

obsession with the Christian movement in Indonesia. Conflict between Christians and Muslims 

had begun in Poso and Maluku32 and infuriated Sungkar. His death served as a critical junction 

in the operational evolution of JI. With Bashir taking control as the 

emir of JI, many of the militant members of JI were unhappy33. They 

felt that Bashir was too willing to accommodate others and too 

moderate on key Islamic political demands34. Among those upset 

were Hambali, Imam Samudra and Mukhlas35. These three created a 

core of internationally networked extremists. 

 

27 http://countrystudies.us/indonesia/22.htm 

28 In 2001, Bakan was renamed Badan Intelijen Negara (BIN) or State Intelligence Agency. The organization was 

reorganized after the 2002 Bali bombings. See 

http://www.rand.org/pubs/monograph_reports/MR1599/MR1599.ch4.pdf, for more information 

29 Ressa, Maria A. “Seeds of Terror; an Eyewitness Account of Al Qaeda’s Newest Center of Operations in 

Southeast Asia” 2003; Free Press Pg.51 30 See www.wikipedia.com/sharia for more information on Sharia Law 31 Sungkar died just three days after arriving back in Indonesia 

32 Also called the Moluccas. See http://www.preventconflict.org/portal/main/maps_maluku_resources.php 33 Sungkar wanted an Islamic state within Indonesia which developed into aspirations of a pan-Islamic Caliphate 

across Southeast Asia. He was obsessed with Christian missionary efforts across the archipelago while Bashir was 

more concerned with the evolution of the Caliphate and promotion of anti-Western interests. Bashir did not feel the 

time was right to begin operations. 

34 International Crisis Group; “How the Jemaah Islamiyah Terrorist Network Operates” 11 December 2002 35 Samudra’s real name is Abdul Aziz and Mukhlas’ name is Ali Gufron. They play a pivotal role in coming attacks. 

12 
Born Abdul Aziz in western Java, Imam Samudra was a star pupil during his time at Islamic 

schools in Indonesia. He was outgoing and charismatic as a youth and was 

enraged, as were most Muslims, by the Soviet invasion of Afghanistan. He 

developed a militant demeanor as he completed school and wanted to join the fight 

against Muslim persecution in Afghanistan. Samudra left home in 1990 and made 

his way to Afghanistan where he learned to fight from the Taliban. After his time 

in Afghanistan, he made his way to Malaysia where he taught at a school run by 

Sungkar and Bashir36. Samudra joined JI in the mid 1990s and would prove to be 

a valuable member in years to come37. 

Ali Gufron He adopted the name Mukhlas 

following his time as a student at the Pondok Ngruki School. Muchlas went to 

Afghanistan and has stated that he met Osama bin Laden in 1987. In 1991, he 

founded a boarding school in Malaysia modeled after his school in Ngruki38. He 

would eventually become the commander of JI’s Mantiqi I. 

 Al Qaeda (AQ) recognized the warm relationship with the newly establish JI and 

sent Omar Al-Faruq to Indonesia to begin coordination and training.39 The 

importance of Al-Faruq in Indonesia at this time can not be understated. AQ had 

developed a comprehensive strategy that included phases before and after 9/11. 

Faruq was instrumental in the development and training of JI fighters and for the 

close coordination between extremist groups in Southeast Asia.40 

With Indonesia in political reform and Bashir at the helm, JI organized and 

continued to develop an extended network across the four Mantiqis and to external groups such 

as Al Qaeda, Abu Sayyaf and the Moro Islamic Liberation Front41. Hambali was active in both 

Malaysia and Indonesia and had close ties to AQ operatives. He was appointed as chairman JI’s 

Regional Shura Council42 and was responsible for coordination of operations and finance for JI. 

Hambali enlisted his counterparts and together they began to develop a plan. 

THE ROAD TO KUALA LUMPUR 

It is fairly easy to identify the key links between AQ and JI. Hambali, Muchlas, and Imam 

Samudra had all been to Afghanistan to either fight the Soviets or to help the Taliban. JI had 

evolved from a concept in the 1980s to a complete organization with a Shura council, regional 

Mantiqis, Wakalahs, and a series of cells throughout the region. Many fighters had also been to 

the southern Philippines to help the Moro Islamic Liberation Front (MILF) and the Abu Sayyaf 

 

36 BBC News; www.news.bbc.co.uk/2/hi/asia-pacific/2499943.stm Monday, 2 June, 2003 37 Imam Samudra would go on to plan the Bali bombing in 2002 and was captured and sentenced to death in 2006. 

38 http://en.wikipedia.org/wiki/Muklas 

39 Omar Al-Faruq was sent to Indonesia to serve as a liaison between JI and AQ. He was also responsible for 

helping the MILF with their struggle against the AFP. He is credited with helping to create the Special Operations 

Group, a paramilitary arm of the MILF. See Abuza’s. “Funding Terrorism in Southeast Asia; Financial Networks of 

AQ and JI” December 200 for more information. 40 Faruq would be captured and sent to Bagram Air Base, AFG. He would escape and eventually be billed in 

Basrah, Iraq by UK Special Forces. 

41 Rabasa et al. “Beyond Al Qaeda; The Global Jihad Movement”; 2006; Rand Corporation 

42 Ratnesar, “Confessions of an Al Qaeda Terrorist”; BIN, “Interrogation Report of Omar al-Faruq”;

13 
Group (ASG) continue their struggle. Access to conflict was a key ingredient in network 

development, and there was an abundance of conflict across Southeast Asia43. 

 Source: Rabasa et al. “Beyond Al Qaeda; the Global Jihad Movement”; 2006; Rand Corporation 

In 1999, violence erupted in Poso and Maluku, Indonesia. Muslim and Christian communities 

traded engagements resulting in almost 5,000 dead over the course of the conflict44. The 

violence continued throughout 1999 and into 2000. This led to 

the creation of two JI paramilitary groups; Laskar Mujahidin45

and Laskar Jundullah.46 The strategic importance over the 

creation of these paramilitary organizations was critical to 

building the combat experience of JI’s members that were too 

young to fight in Afghanistan. On 22 September, the 

predominantly Muslim village of Iha was destroyed by Christian 

militiamen47. These events enraged Hambali, who was now 

planning a meeting with senior AQ member Khalid Sheikh Mohammed and others. The meeting 

was scheduled to take place in Kuala Lumpur in January 2000. Focus of the meeting would 

 

43 With the MILF and ASG battling AFP forces in the Philippines, JI enjoyed a nefarious relationship and access to 

camps. JI also served as a de facto go between in terms of terrorist groups in SE Asia and AQ. Additional separatist 

groups were in Bangladesh, Thailand, and Malaysia creating the nucleus of AQ’s SE Asia expansion. 44 BBC; “Troubled History of the Moluccas”; http://news.bbc.co.uk/2/hi/asia-pacific/806862.stm (as of 11 Feb 08) 45 International Crisis Group; “How the Jemaah Islamiyah Terrorist Network Operates” 11 Dec 02 46 Abuza, Zachary. “Funding Terrorism In Southeast Asia; Financial Networks of AQ and JI” December 2003. 

www.nbr.org 

47 Sejara Indonesia; http://www.gimonca.com/sejarah/sejarah11.shtml ; accessed 3 Feb 08 

14 
presumably be the USS Cole attack48 as well as preparations for what would become the 9/11 

attacks. 

JI was in close coordination with AQ through Hambali and Faruq and an effective strategy 

appeared to emerge. Every terrorist group exhibits several common strategic objectives49. 

Those objectives are threat elimination, compliance, disorientation, attrition, provocation, 

advertisement, and endorsement. By planning a “spectacular” of their own, JI would effectively 

achieve most of these goals in one event. Attrition and disorientation of the Christian population 

would result in threat elimination and eventual compliance. An attack would also serve as 

advertisement that JI was a force with which to be reckoned and a key ally of AQ. This would 

gain AQ endorsement and additional funds to continue Jihad. 

AL QAEDA COMES TO TOWN 

 On a quiet morning in January 2000, several AQ members who had 

just completed training in Karachi, Pakistan accompanied KSM to 

Kuala Lumpur, Malaysia. They would stay with Malaysian JI 

member Yazid Sufaat.50 The meeting that occurred over the next 

few days would steer the course of events to this day. Hambali and 

Sufaat represented JI at what has been called the “2000 Al Qaeda 

Summit”. It is believed that this is where AQ’s global plan was 

explained and the aftermath of the summit correlates with JI’s 

planned operational activities in the coming months. 

It is important to note that the first error in counterterrorism 

operations occurred at this time. The CIA had intercepted a phone 

call from one of the AQ operatives and had requested the Malaysian 

authorities monitor the meeting. Video was taken but audio was not 

available. Without audio, CT officials were left to guess what was 

discussed at the meeting. Additionally, it was some time later 

before anyone noticed Ramzi bin al-Shibh51 was present. Ramzi 

was a known AQ member and roommate of Mohammed Atta52. 

Hambali and Sufaat are connected through several lines. Both had 

been to Afghanistan and fought alongside the Taliban. Both were 

original members of JI and both owned companies connected to JI 

and AQ in the 1990s. 

Source: www.fbi.gov

 

48 http://en.wikipedia.org/wiki/USS_Cole_bombing 

49 Drake, C.J.M.; Terrorist Target Selection; Macmillan Press, 1998; pg 39-44 50 9-11 Commission Report; pg 168. Additionally, Sufaat was the owner of Green Laboratories Medicine and a 

company called InfoTech. Green River Medicine was a front company that enabled JI to acquire explosive 

materials for use across Indonesia and InfoTech hired Zacarias Moussaoui as a consultant. He was paid a monthly 

stipend and sent to Minnesota to work. Moussaoui attended pilot training in Norman, Oklahoma and would be 

called the “20th hijacker” as he was selected to replace Ramzi after Ramzi’s visa was denied 51 Ramzi has often been called the “20th hijacker” as it is believed that he was supposed to be aboard United Flight 

93, the only hijacked flight without 5 hijackers. Ramzi applied for a visa to the United States and was denied at 

least three times. 

52 Atta was one of the 19 hijackers involved in 9/11 

15 
THE EMERGENCE OF MAJELIS MUJAHIDIN INDONESIA (MMI) 

Following the January me

Abu 

at

w

H

H

tea

assu

ashir further alienated JI members when he used MMI to bring a lawsuit against the 

everal meetings between MMI and JI leadership took place throughout 2000. Hambali was 

SSIGNING ROLES AND SETTING GOALS 

hing arms. The MMI-JI relationship was 

 

eting, radical JI operatives began planning for attacks across Indonesia. 

Bakar Bashir was concerning about the timing and repercussions of any 

tacks. This caused significant turmoil within the JI organization as to 

hich direction the group should proceed. The rift between Bashir and 

ambali intensified after Bashir and two former political prisoners 

founded MMI. As Indonesia’s political climate had changed over the 

past two years, Bashir felt it presented new opportunity for dialogue. 

ambali and the radicals felt it was in direct opposition to Sungkar’s 

chings53. Bashir decided that MMI would be the political arm with JI 

ming the organization’s military role.54

B

Singaporean government. The recognition of a non-Islamic judicial system defies the principle 

of Usroh.55

S

growing impatient and turned to Omar al-Faruq. Faruq, at the behest of AQ56, coordinated with 

Hambali and Sufaat to identify and engage targets in Indonesia. More than 30 Christian 

Churches across the country were selected. The motive was twofold; first, retribution for the 

innocent Muslim victims that were killed by Christian militias in Maluku and Poso. Second, it 

coincided with the escalation of violence that AQ had begun making preparations. Bashir was 

still convinced that attacks would bring a wave of repercussions from the Indonesian government 

and the United States. He wanted to remain a training organization until he was sure the moment 

was right. Hambali, Faruq, and JI’s radical commanders opted to begin preparations and were 

convinced they had selected the right targets. Now they needed to assign roles to the Mantiqi 

commanders. 

A

JI had a well developed structure with far reac

established (although strained due to Bashir’s reluctance to move forward with attacks). 

Hambali, as chairman of the Shura, opted to prepare for operations. He and a man named Faiz 

bin Abubakar Bafana57 developed responsibilities across JIs four Mantiqis. Mantiqi I was also 

known as the Malaysian cell and sponsored more than 100 JI operatives ready to carry out 

attacks throughout the region58. Yazid Sufaat, a leading explosives expert, operated the Green 

Laboratory Medicine and would be an important conduit for upcoming attacks59. Mantiqi II 

comprised the bulk of JIs personnel and served as the political base of MMI as well as an 

important recruitment region. The paramilitary groups of JI, Laskar Jundullah and Laskar 

Source: www.indonesia-relief.org

53 International Crisis Group; “How the Jemaah Islamiyah Terrorist Network Operates” 11 December 2002 54 The tactic of a political and military wing with different names is common across the Islamic world. It is used to 

offer legitimacy and publicity to the group’s cause and serves as an advertising station for operations. 

55 International Crisis Group; “How the Jemaah Islamiyah Terrorist Network Operates” 11 December 2002 56 Time Magazine; “Confession of an Al Qaeda Terrorist” 15 September 2002; accessed on 3 Feb 2008. 57 Bafana was a leading figure in JIs Regional Advisory Council and confessed to his part following his capture 

during a raid in Singapore in 2002. See “Singapore Government Press Release on ISA Arrests “11 Jan 02. 

58 Abuza, Zachary. “War on Terrorism in Southeast Asia” Strategic Asia 2003-2004. www.nbr.org 

59 ibid 

16 
Mujahidin60, also contributed to the makeup of this Mantiqi. Mantiqi III would serve as a key 

logistics hub as it included the Philippines and the island of Kalimantan and Sulawesi. These 

islands were main transit points for JI members going to and from MILF and ASG camps in the 

southern Philippines. Finally, Mantiqi IV was a recruitment region for Indonesian exiles on 

Australia and elsewhere. 

With the sharp rise in 

militancy following the fall 

of Suharto, JI was poised to 

strike. They had 

successfully delineated 

responsibilities across a 

nebulous command and 

control structure. Hambali 

set a meeting for October 

2000 to discuss his plan to 

launch attacks on Christian 

churches. The intent was to 

terrorize Christians across 

the archipelago and seek 

revenge for atrocities 

committed by Christians 

against Muslims. This was 

also an opportunity to test JIs 

ability to coordinate a multipronged near simultaneous 

attack. It was a test JI was 

ready to initiate. 

r. 

 

Hambali and Bafana 

purchased explosives in 

Manila for $47,00061 and 

prepared to put into a motion 

a plan that would change the 

movement from ideology 

and rhetoric to action and

terro

60 ibid. Laskar Jundullah and Laskar Mujahidin gained considerable fighting experience during conflicts in Poso and 

Maluku. 

61 International Crisis Group; “How the Jemaah Islamiyah Terrorist Network Operates” 11 Dec 02 

17 
CHAPTER THREE: FROM WORDS TO DEEDS; JI STRIKES 

tren 

uqmanul Hakiem School into a Nationalist-Jihadist-Islamist group capable of waging war. 

 it to Global Jihad. JI was 

rganized, trained and equipped for this mission. It was time to act. 

INTRODUCTION 

It can be said that offense is the best defense. If you do not attempt to stop those who seek to 

destroy all that you have built, then you are forever playing defense. The climate in Indonesia 

during the latter part of the 1990s was one of rebirth. With Suharto’s authoritarian rule ending in 

1998, Indonesia’s internal security apparatus was limited at best. Decentralizing the national 

police force from the military would prove a challenge. The intelligence service was undergoing 

a radical overhaul and the political mindset was one of inclusion and cautious progress. All of 

these factors played a significant part of the internal dynamic that led to JIs cataclysmic 

transformation from the Ngruki ideological school in Indonesia and Malaysian Pesan

L

External factors also played a significant role in JIs development. The introduction of AQ and 

collapse of the Soviet Union tilted the global perspective from a balance of power to a struggle 

against the last hegemony, the United States. Terrorist groups were heading to bin Laden’s call 

for war as a way of gaining endorsement for their cause and tying

o

18 
CHRISTMAS EVE 2000; JEMAAH ISLAMIYAH SENDS A MESSAGE 

Between 8:30 and 10:00p.m., 38 bombs were delivered to Christian institutions across 11 cities 

in Indonesia62. The Christmas Eve church bombings were carefully crafted demonstration of 

JI’s tactical prowess. The bombings were intended to strike fear amongst Indonesia’s minority 

Christian population63. Hambali was the mastermind of the plan and had solicited AQ approval 

through Omar al-Faruq a few months prior64. With AQ’s blessing, Hambali carefully assigned 

ach of his counterparts an area of responsibility. 

an named Zulkufli67 concerning the plan for the Christmas 

ve bombings. 

At approximately 7:15p.m., a

rhetoric and threats to acts of terrorism under the banner of 

Jihad69. 

Church in Central Jakarta. 

l and serves a majority of 

Central Jakarta’s Catholic population. 

 

e

JAKARTA AS GROUND ZERO 

Hambali retained overall control of the Jakarta bombs65. Six targets were selected across the 

city66. Hambali had scheduled a meeting in November 2000, just six weeks before the bombings 

to coordinate the timing of the attack. According to a deposition given by Faiz Bafana, Hambali 

and Bafana met with Bashir and a m

E

 large explosion occurred in front of Koinonia Church in East 

Jakarta. Witnesses saw a thick grey smoke rise from the area and 

the explosion left a crater just over two feet in diameter. The 

bomb was placed in Microlet van parked just outside of the 

church. The driver of the vehicle was killed and a woman nearby 

was injured. The church was guarded at the time and the area 

was fairly deserted with the exception of a few street vendors68. 

With this explosion, JI had officially changed tactics from 

Two additional explosions occurred across town at approximately 8:45p.m. at the St. Kanisius 

The church was full of people attending Christmas Mass and 

wounded five people. According to eyewitnesses, the first 

explosion caused thick black smoke and the second one created a 

large red flame. Both explosions occurred just before the mass 

has ended.70 The St. Kanisius Church was significant because it 

is also a large Roman Catholic schoo

 02 

 Bay, 

 07. Summary of Evidence for Combatant Status Review Tribunal - Subject Hambali. Pg 805. 

l, 

fana. See www.nctc.gov. Zukifli is also a member of the MILF in the Philippines. 

involved in earlier attacks, such as the attempted assassination of the Philippine Ambassador to 

62 International Crisis Group; “How the Jemaah Islamiyah Terrorist Network Operates” 11 December 20 63 Ibid. pg 5. 

64 Time Magazine; “Confession of an Al Qaeda Terrorist” 15 September 2002; accessed on 3 Feb 2008 65 DOD Office of Administrative Review for Detention of Enemy Combatants at US Naval Base Guantanamo

Cuba. 28 Mar

66 International Crisis Group; “How the Jemaah Islamiyah Terrorist Network Operates” 11 December 2002. 

Appendix A 

67 Zukifli bin Hur remains one of the US most wanted terrorists. As a member of JIs regional advisory counci

Zukifli reported to Ba

68 International Crisis Group; “How the Jemaah Islamiyah Terrorist Network Operates” 11 December 2002. 

Appendix A fig 1E. 

69 JI had been 

Indonesia in Aug 2000 and the bombing of the Jakarta Stock exchange in Sept 2000 but not to this level of 

coordination. 

19 
The next two bombings occurred just after the St. Kanisius Church explosions and were the most 

significant in terms of meaning and casualties. First, a large bomb detonated just outside of the 

entrance of the Jakarta Cathedral around 8:55p.m. While it did not cause any casualties, the 

cathedral is the largest in Central Jakarta and was full of worshippers at the time of the 

explosion. Police investigators discovered another 8kg bomb outside of the Cathedral that had 

not detonated. The bomb was rigged with an alarm clock as a trigger.71 Had this bomb went off, 

casualties would most certainly have been more significant. 

The second explosion occurred at Santo Yosef Church in 

the Jatinegara District of East Jakarta. The bomb exploded 

at 8:55p.m., just as patrons were departing the Christmas 

Mass. The bomb killed four people and wounded at least 

eighteen others. Particularly significant about this bomb 

were the substantial bits of metal from the explosion that 

caused many of the injuries72. The detonations also 

damaged fourteen vehicles, one food stall and a bus stop shelter. The attack at Santo Yosef 

Church was the deadliest of the Jakarta bombs. 

The final two bombs in Jakarta were placed at the Oikumene Protestant Christian Church and the 

Anglican Church. The Oikumene explosion left a crater one 

and a half feet in diameter and two inches deep73. Church 

services were underway and a four-year-old girl was 

wounded in the attack. Panicked worshippers rushed out of 

the Church after seeing smoke appear under the front door 

and through a window. Jakarta police were able to find and 

diffuse a bomb discovered at Anglican Church, just down the 

street from St. Kanisius Church74. 

While the attacks in Jakarta did not have the intended level of destruction, Hambali had 

succeeded in orchestrating a coordinated near-simultaneous attack across the city. The 

disorientation and fear spread by his plan surely met JIs expectations. 

 70 International Crisis Group; “How the Jemaah Islamiyah Terrorist Network Operates” 11 December 2002. 

Appendix A fig 1B 

Source: asiamaya.com 

71 The Jakarta Post; “Terror Attacks; the Positive Outcomes” 26 Dec 02. Accessed on 8 Feb 08. 72 ibid 

73 International Crisis Group; “How the Jemaah Islamiyah Terrorist Network Operates” 11 December 2002. 

Appendix A fig 1B 

74 The Jakarta Post; “Police Baffled by Bombers’ Tactics” 2 Jan 01. Accessed on 10 Feb 08. 

20 
MEDAN

If the Jakarta bombs were a signal of JIs coordination strength, the explosions in Medan signaled 

e country. There was a meeting held by JI operatives in October 2000 and 

chaired by Hambali. The meeting took place in Kuala Lumpur and, amongst 

other issues, divided responsibilities for bombings across Indonesia. At this 

meeting, Yazid Sufaat was given responsibility for Medan

JIs reach across th

ely, nine of the bombs had failed to detonate and were discovered and 

iffused by police77. 

 the 

edan bombings, a powerful message was sent. JI had demonstrated the willingness to act. 

Batam Island is part of the Riau 

 instructions and the encouragement 

om Hambali, Samudra selected four targets for the attack. 

was ongoing. No one was injured in the Batam bombings. Samudra later stated in his deposition 

 

75. Sufaat was 

known for housing the Al Qaeda operatives earlier in 200076. His ownership 

of Green Laboratories Medicine afforded him the resources and access to 

chemicals to complete his charter. Sufaat made preparations and began to 

examine Medan. Medan is a large city located on the island of Sumatra. It is 

home to more than 2.5 million inhabitants and several targets were selected. 

Confirmed bombs at 11 churches were evidence enough that Sufaat and JI 

had carefully timed the attacks to coincide with the Jakarta and Java 

explosions. Fortunat

d

Two explosions were successful at the Protestant Church of Indonesia and the Cathedral Church, 

both in Medan. Both explosions resulted in no injuries. Although no one was killed during

M

BATAM 

Islands Province of Indonesia78. It serves as a major transit hub 

between Singapore, Malaysia, and Indonesia. It is accessible 

by both ferry and air travel. Imam Samudra had come to call 

Batam his second home79. It was no surprise when Imam 

Samudra was given responsibility for the Christmas bombings 

on Batam. Samudra stated in his deposition several years later 

that he selected Batam because of its easy access to 

surrounding counties of Malaysia and Singapore. Hambali 

came to visit Samudra on Batam just days before the attacks to 

offer motivation and encouragement. Mantiqi I commander 

Mukhlas also visited to offer last minute instructions for the 

campaign80. With current

fr

At approximately 9:00p.m., there were several explosions observed at the Simalungan Protestant 

Christian Church, the Bethel Indonesia Church, the Pentecostal church of Indonesia, and the 

Santo Beato Church. The explosions were small in nature and occurred while Christmas Mass 

75 Turnbull, Wayne “A Tangled Web of Southeast Asian Terrorism; the Jemaah Islamiyah Terrorist Network” 31 Jul 

03. Monterey Institute of International Studies, Monterey, CA. 

http://www.terrorismcentral.com/Library/terroristgroups/JemaahIslamiyah/JITerror/WJ2000.html 76 See chapter 2 “Al Qaeda Comes to Town” 

77 CNN.com “Indonesian President condemns Christmas Eve Church Bombings” 25 Dec 00. accessed of 10 Feb 08 78 Wikipedia.org/Batam 

79 Murphy, Dan; “Cooperation Nets Terrorist Suspect” Christian Science Monitor 5 Feb 03. See http://www.kabaririan.com/pipermail/kabar-indonesia/2003-February/006696.html. accessed on 13 Feb 08 80 ibid 

21 
to Indonesian authorities that the bombings on Batam were linked to the bombings across 

Indonesia and served as JIs “coming out party”81. 

AFTERMATH 

The aftermath of the coordinated bombings on Christmas Eve of 2000 resulted in 19 people dead 

and over 150 injured. The targets were spread across the archipelago and spanned thousands of 

miles. Thirty-Eight bombs were placed at Christian churches and homes and all thoughts 

pointed to terrorism. Fear and anger spread throughout the 

Christian community. JI had successfully initiated a plan to further 

isolate Indonesia’s Christian population from the Muslim majority. 

Abu Bakar Bashir denied any involvement in the bombings and 

attempted to infuse a sense of violence in Indonesia’s Muslim 

population. Fresh memories of the fighting in Poso and Ambon 

and the conflict in Aceh all played key roles in the destabilization 

of internal Indonesian relations. 

 

CONCLUSION 

Although most of the bombs were unsuccessful in creating the level of destruction and carnage JI 

had hope to accomplish, the message that JI was a force capable of large-scale coordinated 

attacks should have been clear. The initial aftermath had police and intelligence agencies 

looking in every direction. No accusations were directed at JI until years later when the 

investigation into the Bali bombings of 2002 revealed a common cast of actors that all belonged 

to JI. JI was not even considered a terrorist group in 2000 despite the many indicators it 

presented. The fact that these indicators were not discovered and examined remains a significant 

counterterrorism failure. The most difficult part of counterterrorism is to identify those pieces 

prior and enact countermeasures prior to the actual act. 

81 ibid 

22 
CHAPTER FOUR: TERRORISM; EXAMINING ALL THE PIECES 

INTRODUCTION 

The intent of this paper is to understand the multitude of issues that allowed the concept of JI to 

evolve from rhetoric to action. By understanding the political, social, economic, and religious 

dynamics that drive a subculture to militancy, action can be taken to recognize and address 

terrorism before it has a chance to occur. 

This chapter will examine the fundamental aspects of terrorism that JI exhibited prior to the 

Christmas Eve church bombings of 2000. Understanding that terrorism is not just action but the 

fundamental desire to inflict casualties in order to promote a political agenda (in this case the 

establishment of NII and alignment with AQ) is paramount. Finally, establishing a groups status 

as a terrorist group, countermeasures should be applied in the form of an effective 

counterterrorism policy to, hopefully, prevent the next Bali before it occurs. 

23 
DEFINING TERRORISM; THE CASE OF JEMAAH ISLAMIYAH 

In every militant group like JI, there are flags that appear along the way. These pivotal 

indicators are often subtle and overlooked. A history of political violence, a struggle for 

autonomy that no one noticed, an authoritarian ruler, or an intense belief in a charismatic leader 

all played a pivotal role in the terrorist paradigm and must be examined. 

Using JI as a model, there are four elements that should be studied when determining their status 

as a terrorist group before the Christmas Eve church bombings82. The 

four elements are premeditation, political motivation, the targets are 

noncombatants, and that JI was a sub national group before the 

bombings. There is no implication that these attacks could have been 

prevented but rather how to examine the indicators that may have 

expedited arrests before the events in Bali in 2002. This very 

important distinction must be made prior to contemplating the range of 

options against the group. 

The first element is premeditation. Did JI intend to commit the Christmas Eve bombings? 

Based on earlier chapters, it is fair to say that premeditation was obviously 

present. Hambali had sought approval for the bombings more than four 

months prior. Securing the funds that would ultimately be used to purchase 

materials and explosives also qualifies as premeditation. Hambali assigned 

responsibilities to specific cities and even visited the commanders 

responsible for the bombings days prior to the attacks. Imam Samudra had 

arranged for Singaporean JI members to come to Batam and help prepare 

for the attacks83. Yazid Sufaat had ordered the ammonium nitrate used in 

Medan through his Green Laboratories Medicine company months prior to 

the attacks. All of these instances constitute premeditation. 

The second element is political motivation. Abu Bakar Bashir’s radical teachings at Pondok 

Ngruki and in Malaysia were, above all, politically motivated. Religious ideology that spawns 

nationalistic goals is political. Bashir went so far as to sue the 

government of Singapore for having a non-Islamic legal 

system84. The goal of establishing NII is a macro concern and 

serves to change a larger order, in this case the type of 

government from a republic to an Islamic State. Hambali’s 

hatred of the West (acquired in Afghanistan from AQ) is also 

politically motivated. Adopting the AQ model, Hambali was 

enraged by the presence of United States’ soldiers in Muslim 

lands. This started with the American presence in Saudi 

Arabia in 1990 and continued through 2000. 

 

82 Pillar, Paul R. “The Dimensions of Terrorism and Counterterrorism”. 2001. Terrorism and Counterterrorism; 

Understanding the New Security Environment. Pg 24-27. This entire section is derived from Pillar’s definition of 

terrorism. 

83 Christian Science Monitor “Cooperation Nets Terror Suspect” Feb 03 84 International Crisis Group; “How the Jemaah Islamiyah Terrorist Network Operates” 11 Dec 02

24 
The third element of defining a terrorist group is the target set should be noncombatants. JI 

never attacked the Indonesian military. All of JIs attacks have deliberately focused on either 

Western tourists or the Christian minority. The Christmas Eve 

church bombings killed 20 noncombatants and injured more than 

150 others. Hambali specifically addressed selecting “soft 

targets” in early 2000 to Omar al-Faruq and was granted 

permission, presumably from senior AQ leaders85. This tactical 

strategy was a deliberate and calculated method to eliminate as 

many Christians (and would eventually lead to targeting 

Westerners in Bali, the Marriott Hotel in Jakarta, and the 

Australian Embassy) without compromising JIs strength. 

The fourth and final element is the perpetrators are sub national groups or clandestine agents. JIs 

had a well defined organizational structure that began with Bashir as the Amir and continued 

down the chain from the Regional Shura Council through the 

Mantiqis. Each Mantiqi had an assigned area of 

responsibility and administrative roles within JI86. This level 

of hierarchy proves that JI had a functioning command and 

control which allowed it to promote its political, military, and 

societal agenda which was the establishment of the Islamic 

State of Indonesia (NII). 

Above everything else, Jemaah Islamiyah demonstrated the political motivation that led to the 

development of a highly organized structure that in turned planned attacks against noncombatant 

targets. The choice to take up arms in opposition of a political process is a premeditated one. 

Each element is linked and identifying any one of the elements could have led to increased 

surveillance and possible interdiction prior to the Christmas Eve attacks. 

 

85 Ratnesar, “Confessions of an Al Qaeda Terrorist”; BIN, “Interrogation Report of Omar al-Faruq”; 86 The administrative roles were based on the resources available and the geographic region. Mantiqi I was 

primarily the economic region because of front companies in Singapore and Malaysia. Mantiqi II was the conflict 

region as it encompassed all of Java and Sumatra as well as the surrounding islands. Mantiqi III was the training 

region because of the Philippines and access to MILF/ASG camps in Mindanao. Mantiqi IV was a recruitment and 

advertisement region. 

25 
FROM STRUGGLE TO JIHAD; A CONDITIONAL OXYMORON 

The struggle for an establishment of the Islamic State of Indonesia (NII) is not new. Since the 

Darul Islam Rebellions (1949-1962), a small portion of the Muslim population has pushed for 

change. The Darul Islam movement was suppressed by Suharto’s regime and forced 

underground in the mid 1960s87. It is out of this movement that JIs push for NII was spawned. 

Suharto’s government was highly centralized and 

opposition movements were quickly extinguished. The 

conditions for underground struggle and the development 

of JI were ripened when Sungkar and Bashir were 

arrested for teaching what was deemed subversive 

ideology at Ngruki. The arrests sparked protests and the 

ensuing political turmoil ended with a reduced sentence 

for both Sungkar and Bashir88. Following their release 

from prison, Sungkar and Bashir went to Malaysia and 

founded the Luqmanul Hakiem School. With the creation of this pesantren89, JI had just gone 

international. Known terrorists Mukhlas and Imam Samudra also taught at the Luqmanul 

Hakiem after in the mid-1990s. It is here in Malaysia where the radical ideology of JI changed 

from realization of NII to a Jihadist-Islamist-Nationalist hybrid variant. In 1998, Sungkar and 

Bashir returned to Indonesia but the Luqmanul Hakiem School remained open and continued the 

ideological teachings of Bashir. 

This history of struggle is important when addressing the question of the strategic choice 

approach to terrorism as a viable political option. Once the decision is made to use terrorism for 

strategic reasons, most terrorist organizations are impatient90. The intense desire to shift from 

rhetoric and words is caused by dynamic factors such as organizational pressures and the 

appearance of vulnerability in an adversary. 

The organizational pressures were an internal conflict 

within the core of JIs hardliners. Fresh from the 

fighting in Afghanistan and reinvigorated by conflicts 

in Poso and Maluku, Hambali, Mukhlas, and Imam 

Samudra felt the time was right to begin operations. 

Bashir was concerned about timing and retaliation from 

the West as well as the Indonesian government. The 

era brought enormous pressure to gain AQ endorsement 

and, more importantly, secure valuable AQ funding 

which also fed the sense of urgency to act. 

 

87 Koschade, Stuart. “A Social Network Analysis of Jemaah Islamiyah; The Applications to Counterterrorism and 

Intelligence” 14 Oct 05 88 Mobley, Blake. “Jemaah Islamiyah Dossier”. 26 Aug 04. Center for Policing Terrorism 89 Pesantren or Pondok Pesantren are Islamic boarding schools in Indonesia. According to one popular tradition, the 

pesantren education system originated from traditional Javanese pondokan; dormitories for Hindus to learn martial 

arts and meditation. Source: wikipedia.com/pesantren 

90 Crenshaw, Martha. “The Logic of Terrorism: Terrorist Behavior as a Product of Strategic Choice”. 1998. 

Terrorism and Counterterrorism; Understanding the New Security Environment. Pgs 54-59. This section is derived 

from Crenshaw’s logic of terrorism. 

26 
The Indonesian government was in a state of upheaval following Suharto’s resignation from 

power in 1998. As if overnight, the highly centralized government seemed to experience a 

period of reinvention. The separation of the national police force from the Angkatan Bersenjata 

Republik Indonesia (ABRI)91 provided the incentive for JI to evolve. The decentralization 

process presented opportunities for opposition movements that had been long suppressed. A 

political competition began amongst militant Muslim groups to further their respective agendas. 

JI had evolved from wanting just the establishment of NII to the creation of a pan-Islamic state 

spanning a significant portion of Southeast Asia. The race to have a place in the political 

spotlight between movements such as DI, GAM, and JI culminated in a tinder box primed for 

terrorist development. 

USING THE NEW TERRORSM MODEL 

A key part of Jemaah Islamiyah’s aligning with AQ is the understanding of their part in AQs 

Global Jihad. How did JIs mindset in 1999-2000 align within AQs grand strategy? In order to 

answer this question, we must understand the mindset of the modern terrorist and examine the 

six key distinctions as they relate to JI92. 

Today’s terrorists are more violent. In the case of JI, the concept of the Darul Islam Rebellions 

was significantly radicalized by the Soviet invasion of Afghanistan and the teachings of Bashir at 

Ngruki and in Malaysia. The struggle of the establishment of an NII against an oppressive 

government gave way to violent anti-West and anti-Christian 

ideologies. Militant Muslims in Indonesia initially wanted a seat at 

the political table and avoided significant attacks on civilians to 

avoid isolating the general public. JI adopted a much more radical 

approach. Fresh from fighting in Afghanistan and frenzied by 

Bashir’s rhetoric, the new breed of terrorists, figures like Hambali 

and Mukhlas, adopted a much more violent strategy of killing as 

many “infidels” as possible without regard to the political process 

affected. They did not want a seat at the political table, “they wanted to destroy the table and 

everyone sitting at it”93. 

JI defined the concept of a transnational non-state actor. The ideology of JI was local in terms of 

the establishment of an NII but had an overarching goal of enveloping Southeast Asia in a 

greater pan-Islamic Caliphate. Porous borders and frequent travel between JI cells in Malaysia, 

Singapore, the Philippines, and Thailand, as well as training in Afghanistan and Pakistan made JI 

a global operation. The idea of JI being the Southeast Asia regional head of AQs nexus seemed 

to be based on Fortune 500 Company’s prospectus. JI had transformed the face of Indonesian 

militant Islam from local struggle to Global Jihad. 

Financing is another key distinction that set JI apart from its predecessors. The original Darul 

Islam Rebellions relied on local militants to continue the struggle for NII. There was no 

organized “resistance fund” or any semblance of central coffers with which to wage battle. JIs 

evolution was intricately tied to funding and organization. As an example, Hambali paid 

 

91 The ABRI became the Tentara Nasional Indonesia (TNI) during a massive reorganization following the Suharto 

regime. The intent was to remove the TNI from politics which was completed in 2003. 

92 Howard, Russell D. “Understanding Al Qaeda’s Application of the New Terrorism-The Key to Victory in the 

Current Campaign”. 2003. Terrorism and Counterterrorism; Understanding the New Security Environment. Pgs 75-

83. This section is derived from Howard’s six distinctions of the new terrorist. 

93 Quote attributed to former CIA director James Woolsey, 1994. 

27 
$47,000 for explosives used for the Christmas Eve bombings. This is in addition to his front 

company Konsojaya that was used for operation Bojinka in 1995. Yazid Sufaat had two known 

front companies in Malaysia and hosted the AQ summit in 2000. AQ is known to have funneled 

funds to JI for use in terrorist operations. Travel was common to and from the region and on to 

Pakistan for additional training. The structured organization with Mantiqi I in charge of finances 

proves JI had the technology, the means, and the desire to move forward with its terrorist agenda. 

Senior JI differed from “old terrorists” in terms of training as well. Camps in Pakistan and 

Afghanistan offered significant experience in hand combat, 

explosives, weapons, and guerilla tactics. JI benefited from the 

revolving relationship with AQ. JI often sent new recruits to 

train in these camps and these new fighters formed the nucleus of 

JIs militant circle. The creation of Laskar Jundullah and Laskar 

Mujahedin for operations in Poso and Maluku allowed fighters to 

rapidly learn techniques and procedures that would prove 

beneficial in years to come. Recurring training at camps run by 

the MILF and ASG also offered the remaining requisites that 

culminated in a dedicated, well-trained fighter capable of waging Global Jihad. 

One of the most important factors of JI is its resistance to penetration by authorities. This is 

because of the intricately balanced network of relationships cultivated by interfamily marriages 

of JI members. This is done for two important reasons. First, it ensures undivided loyalty of the 

member. Second, it creates a hierarchal family that it nearly impossible to infiltrate. Noordin 

Mohammad Top also taught at Luqmanul Hakiem with Mukhlas and Bashir94. It was here and at 

Ngruki that JI conditioned its recruits to absolute compliance. When this was achieved, JI 

carefully crafted a series of marriages between cell leaders and daughters of other JI members. 

As part of the recruitment phase, friendships were started and family was stressed as the most 

fundamental important part of JI. This led to arranged marriages to ensure connection to JI as a 

family. Another reason JI is so difficult to penetrate is its rigid cell structure. Cells report 

directly up a chain through the Wakalah to the Mantiqi. The Regional Shura Council coordinates 

all activities and determines courses of action. 

 

94 Top’s name is purposely omitted from the majority of this paper because he does not become a significant factor 

until after Bali 2002. 

28 
The final distinction between JI and its predecessors is the access to weapons. While JI does not 

possess actual CRBN WMD, it did have access to large volumes of automatic weapons and 

chemical used to create explosives. With access to these items and training conducted as 

mentioned above, JI would prove to be a formidable force to be reckoned with in years to come. 

A WORD ON RELIGION 

Darul Islam taught of an independent Islamic state. Local villagers gathered and listened as the 

local Imam spoke of the golden days of Islam. Following World War II, 

the push for independence from Dutch rule resulted in an oppressive 

government under Sukarno. When Suharto came to power in 1965, there 

was once again hope for an Islamic state. This was also dismissed and 

Suharto dissuaded opposition in the form of swift military or police action. 

The rise of Pondok Ngruki led to thoughts of militant opposition to any 

concept other than Islam and Sharia law95. 

The Soviet invasion of Afghanistan saw scores of fighters from Indonesia and throughout 

Southeast Asia flock to join the fight against the infidels. When these fighters returned, they had 

a renewed fervor and combat experience to counter Indonesia’s authoritarian rule. Conditions in 

the world were changing and the emergence of the media in the form of the internet and satellite 

television created a cultural revolution of sorts. No longer were skirmishes local in nature, they 

were now headlines available for anyone to see with the click of a mouse or flip or the remote 

control. 

The ability to promote and spread a militant religious agenda became much easier. Islamic 

websites and television programs began to appear. Militant Muslims recognized this new front 

and moved throughout the late 1990s to establish a religious foothold on the new battlefield. 

AQs brand of Salafi-Wahhabi Jihadi appealed to young militants. The power of the new Islamic 

order and defiance of the West portrayed an image of strength. Salafism is often misused 

interchangeably with Wahhabism. Salafism in its most 

simplistic form is the rejection of all things West and the 

establishment of an uncorrupted, pure Islamic religious 

community96. Wahhabism is named after an 18th century 

reform movement and treats the Quran and Hadith as 

fundamental texts97. AQ has taken a hybrid version of both 

sects of Islam and morphed it to fit its needs. The power of 

AQ in shaping the fundamental mindset of JI members began 

in the 1980s when JI members went to Pakistan and 

Afghanistan. The militancy and zeal permeated through the ranks and JI members brought that 

mindset home to Indonesia and Malaysia. This religious zeal, combined with Darul Islam, 

created the modern JI Jihadi. These key JI leaders spread this ideology at Ngruki and Luqmanul 

Hakiem creating a new core of JI members. 

 

95 Ranstorp, Magnus. “Terrorism in the Name of Religion” 1996. Terrorism and Counterterrorism; Understanding 

the New Security Environment. Pgs 125-135. This section is derived from Ranstorp’s chapter. 96 http://en.wikipedia.org/wiki/Salafi. accessed on 15 Feb 08 97 http://en.wikipedia.org/wiki/Wahhabism. accessed on 15 Feb 08 

29 
Suicide bombing in the name of Islam gained significant notoriety throughout the late 1980s and 

into the 1990s. The terrorist groups Hezbollah and Hamas had successfully countered Israel’s 

arsenal with human weapons. Suicide bombers are the ultimate “fire and forget” smart weapon. 

They do not require position updates nor abort codes. They can avoid barriers as they arise and 

nearly always strike their intended target. The most difficult part of 

the entire process is conditioning a society to enhance recruitment of 

new weapons. The campaign began in the madrassa with the local 

cleric “selling” the notion of Martyrdom. The cleric draws on a few 

stories from the Quran and translates them into a modern 

rationalization. The students are slowly conditioned into acceptance. 

On the second front, the Islamic media does not portray the suicide 

bomber as a terrorist but rather a Martyr for Islam, one answering the 

call to continue the struggle. The terrorist group finances the family of the bomber and 

celebrates his life and the “achievement” of Martyrdom. Tales of virgins and glorious paradise 

are circulated to make death seem more attractive. To an oppressed society, this can be an 

appealing and lucrative option. The choice between living a life in a refugee camp in Gaza with 

days spent in anonymity and being glorified and celebrated as a hero of the cause becomes much 

more rationalized. The most perplexing aspect of this phenomenon is the widespread acceptance 

by Muslims around the world and the proliferation of new suicide bombers outside of the Middle 

East98. JI recognized the value of suicide bombers and prepared them for attacks in the coming 

years. 

CONCLUSION; PUTTING IT ALL TOGETHER 

This chapter examined whether or not JI should have been considered a terrorist organization 

before commencing the attack on Christmas Eve. Attention was given to the defining terrorism 

according to four critical elements; premeditation, political agenda, target selection, and an 

organized group. Understanding the conditions that lead a group like JI to engage in terrorist 

activities is often the result of an intense desire to act based both on internal organizational 

pressure for results and the appearance of weakness in an 

adversary, in this case the transitioning Indonesian 

government. Additionally, interaction with AQ developed a 

new kind of terrorist, one that is more violent than his 

predecessor, better trained, better equipped, better financed, 

and part of an organization that is better organized. Finally, 

special attention was given to the basic role of religion and 

how it relates to the modern JI Jihadi in terms of historical 

Darul Islam, to the rise of militancy following participation in 

operations in Afghanistan. Emphasis was placed on AQs hybrid Salafi-Wahhabi version of 

Islam and the role and rationale of suicide bombing. 

 

The goal of this chapter is to understand that JI presented every flag mentioned in this chapter 

prior to the Christmas Eve bombings. While it is easy to dissect the indicators that presented 

yesterday, there is hope that similar indicators would be recognized today and prevent attacks 

tomorrow. 

98 The LTTE actually proliferated suicide bombers as part of their campaign against the Sinhalese majority in Sri 

Lanka. This paper focuses on the Muslim propagation of suicide bombers and how they relate to JIs decision to use 

suicide bombers for their operations in the name of Islam. 

30 
CHAPTER FIVE: THE EVOLUTION OF COUNTERTERRORISM 

 Source: asiatimes.com

INTRODUCTION

In order to understand how JI was so successful until 2005, you must understand Indonesia’s 

ever evolving CT policy and its political history. To better grasp this concept, this paper will 

very briefly examine Indonesia’s political history under President Suharto from 1965-1998. The 

link between the decentralization of government, politics, the military, and the National Police 

caused by Suharto’s fall and the rapid development of Jemaah Islamiyah is unmistakable. 

This final chapter will also examine Indonesia’s current CT Policy and formulate a theoretical 

road map for the future. In order to avoid the Bali Paradox, CT must evolve before an attack 

based on a sound intelligence program, an effective information operations campaign, and a 

highly adaptable military and police force capable of responding to the full spectrum of terrorist 

activities. 

31 
POLITICAL HISTORY 

On 30 September 1965, six prominent Indonesian generals were abducted and murdered. The 

regime of President Sukarno was backed by the military and Indonesia’s communist party. 

Sukarno blamed the assassinations on the Indonesian Communist Party99. The assassinations 

and following turmoil became known as Indonesia’s “Black September”. What followed was a 

slow coup d’état that resulted in a named Major General Suharto taking control of the country. 

Suharto quickly consolidated power amongst two distinct groups; the military and the 

bureaucratic elite. The first priority was to eliminate dissention 

amongst opposition groups. The result of this action was one of the 

world’s worst human rights violations with estimates of anywhere 

from 100,000 to 1 million Indonesians killed100. What transpired 

was the creation of a strict political system. Only three political 

parties were recognized as viable to the central government. They 

were the government party called the Golkar, the Muslim United 

Development Party (PPP), and the Christian Indonesian 

Democratic Party (PKI). Every person from a local magistrate to national representative had to 

undergo a background security check and be approved by the government. Suharto’s regime had 

effectively centralized Indonesia’s entire government. 

Indonesia experienced an economic boom in the 1970s that was due to Suharto’s reinvestment of 

oil revenues into agriculture, infrastructure and education101. The intent of the authoritarian 

regime was to satisfy Muslim demands and continue to build Indonesia’s base as a political 

entity within Southeast Asia. Suharto was attempting to depoliticize the militant Muslims still 

present from the Darul Islam Movement. 

The Islamic revival of the 1970s can be attributed to the actions of the Palestinian Liberation 

Organization (PLO)102 and the Wahhabi expansion from Saudi Arabia in the form of Islamic 

charities and relief organizations. The simultaneous expansion of terrorism and Islamism 

provided a perfect flash point for militant Muslims. The Saudi organizations built mosques and 

am according to the Wahhabi view. The ongoing urbanization and 

ing middle class in Indonesia made access to these views significantly 

re available. In 1971, Sungkar and Bashir had established the pesantren 

 Ngruki and began teaching a similar form of Wahhabism. They taught 

haria law was the only law and to object to anything not pure Islam. In 

975, Muslim students at a university nearly 70 miles from Ngruki 

e and demand changes. Suharto feared this increasingly radical view 

would gain acceptance in the PPP, the only approved Muslim political party in Indonesia. He 

sought to prevent the radicals from gaining seats in the upcoming election by having his 

intelligence chief covertly assist DI members in establishing a group known as Kommando 

Jihad

distributed books on Isl

increas

mo

at

S

1

began to protest the regim

 

103. The onset of “Islamic Terrorism” blamed on Kommando Jihad convinced Indonesia’s 

99 Conboy, Ken. “Kopassus; Inside Indonesia’s Special Forces” 2003 Jakarta, Indonesia pg 127-142 100 Bambang S. et al. “The Devious Dalang: Sukarno and the So-Called Untung Putsch” 1975. An eyewitness 

account of the military coup in Indonesia in 1965 101 Ressa, Maria A. “Seeds of Terror; an Eyewitness Account of Al Qaeda’s Newest Center of Operations in 

Southeast Asia” 2003; Free Press. Pg.47 102 The PLO gained instant worldwide recognition in 1972 for their actions in Munich. While the operation was a 

failure for the operatives, it was a dramatic success for the PLO in terms of media and message. 103 Van Bruinessen, Martin. “Genealogies of Islamic Radicalism in post-Suharto Indonesia” 2001 

32 
generally moderate population not to vote for PPP members. In effect, Suharto had Kommando 

Jihad created as a scapegoat and to divert attention from the premeditated security crackdown. 

 

Turning his sights to the university, Suharto’s government banned the protests and identified 

Sungkar and Bashir as DI faction members attempting to subvert Indonesia’s population. Both 

men were sentenced to nine years in prison and released early on appeal in late 1982. In 1984, 

militant Muslims, some alumni of Ngruki, began to protest and drew the attention of Suharto’s 

regime. When it was discovered that there were links to Sungkar and Bashir, both men were 

notified their appeals were overturned and they would return to prison to complete their 

sentences. Sungkar and Bashir fled to Malaysia in 1985. 

The mid 1980s saw affluent Muslims graduate to politics and most opted to join the Golkar 

party104. These people were students of the 1960s and had protested the Communist party and 

the old regime of Sukarno. They were also moderate Muslims that would serve as an excellent 

counterbalance to the radical views of Wahhabi Islam beginning to permeate 

Indonesia. What Suharto failed to see what the actual “greening” or infusion of 

Islamic representation of the Golkar party. The revolution in Iran also changed 

many of the moderates view on Islam. What had always been about tradition 

evolved into what change could bring to Indonesia. Finally, the travel of 

hundreds, if not thousands of Indonesians to Pakistan and Afghanistan in the 1980s would 

ultimately change the political face of Indonesia in coming years105. 

The absolute control of power by Suharto and his inner circle maintained a stranglehold on the 

Indonesian political climate throughout the 1980s and into the early 1990s. As long as there was 

economic growth and prosperity, it seemed most Indonesians were content to continue with daily 

life. The mid 1990s saw a significant shift from moderate views and content to more radical 

views and contempt. The loss of the Soviet Union as a superpower shifted all eyes toward the 

US as the imperialist country forcing terms for trade and ideals. Radical Islam had found an 

enemy in the US but Suharto’s regime kept this increasing anger at bay. Muslims returning from 

Afghanistan began to preach a highly militarized version of Islam. 

The economic crisis of 1997-1998 in Southeast Asia devastated Indonesia’s economy and 

resulted in widespread unemployment. When Suharto 

was forced from office, 33 years of authoritarian control 

on all facets of politics came to an end. The 

decentralization process would take several years to fully 

segregate duties and responsibilities. The intelligence 

agencies were left in shambles, the military and the 

National Police were decentralized and split into two 

distinct groups. Political reforms offered the perfect 

opportunity for militant Islamic movements, fueled by the 

fatwa of bin Laden, to vie for the political center stage. It 

would take four years to fully complete the transition of 

power to the proper agencies within the government. JI 

seized this opportunity and unleashed four years of terror. 

104 The primary reason was the PPP had received significant derogatory press coverage due to the actions of 

Kommando Jihad. It was an easier option to join the government party Golkar. 

105 Van Bruinessen, Martin. “Genealogies of Islamic Radicalism in post-Suharto Indonesia” 2002 

33 
INDONESIA’S INTELLIGENCE APPARATUS 

Indonesia, recognizing the failure of intelligence in the 2002 Bali bombings, conducted a 

complete reorganization of existing intelligence agencies. They were aligned along three critical 

venues: the state intelligence agency (BIN), the military’s strategic intelligence agency (BAIS), 

and the national police intelligence, as well as elements in the Justice and Finance Ministries106. 

Each of these agencies play a crucial role in counterterrorism operations. 

Indonesia’s State Intelligence Service (Badan Koordinasi Intelijen Negara) or Bakin was 

Indonesia’s primary intelligence service until its reorganization in 2003. Bakin had little interest 

in JI prior to 2001 and did not view them as a direct threat to internal 

security. Bakin viewed JI as little more than a DI offshoot107 with similar 

nationalistic goals. In 2003, the reorganized Indonesian State Intelligence 

Agency (Badan Intelijen Negara) or BIN became responsible for foreign 

and domestic collection and analysis. BIN agents primary role in the case 

of JI is the monitoring the activities of foreign jihadists arriving in 

Indonesia and their association with JI members. This requires extensive 

cooperation both internally, among the military and national police 

agencies, and externally, amongst foreign intelligence agencies and 

international police agencies such as Interpol108. BIN agents are also monitoring travel of 

potential fighters from Indonesia to and from the Middle East. The critical dynamic is the 

sharing of information in a timely matter between international intelligence agencies and within

s own services for domestic operations. 

Department of Defen

al Commands. BAIS is also forging better relations with BIN 

nd the national police agencies. 

crime, narcotics trafficking, and more common criminal activities111. The POLRI can be of 

 

it

The Tentara Nasional Indonesia (TNI) is the Indonesian equivalent to the United States 

se109. It consists of departments from the Army, Navy, and Air Force. 

Additionally, the TNI also contains the Strategic Intelligence Agency 

(BAIS). The primary function of BAIS during the Suharto era was 

counterterrorism. With the collapse of Suharto’s regime and the ensuing 

decentralization of the government, the national police assumed the duties 

of domestic intelligence and CT. BAIS maintained a somewhat active 

program but many of the BAIS officers transferred to the national police 

agency and information gaps made JI’s continued development much 

easier throughout the government transformation in 1998-2000. BAIS has 

recently revamped its domestic intelligence capability and, in 2005, developed a domestic CT 

desk within the agency110. The department consists of six officers that have focused on 

developing intelligence on potential terrorists, especially those associated with JI, and furthering 

the relationship with the Territori

a

The Indonesian National Police formally separated from the TNI in 1999 and developed its own 

domestic intelligence agency (POLRI). The agency, however, is primarily focused on organized 

106 Wise, William. “Indonesia’s War on Terror” Aug 05. United States-Indonesia Society 107 Conboy, Ken. Intel; Inside Indonesia’s Intelligence Service” 2004 Jakarta, Indonesia pg 204-207 108 Longwarjournal.com except on cooperation with Interpol during the hunt for Mohammed Noordin Top, a senior 

JI commander captured in June 2007. 

109 Indonesia also has a Department of Defense. This comparison is for simplification purposes only. 110 Wise, William. “Indonesia’s War on Terror” Aug 05. United States-Indonesia Society. Pg. 53 111 Ibid pg 53-54 

34 
significant value at the local village or city and district level as the agency is the most 

widespread throughout the country. 

Additional CT elements in the Ministries of Justice and Finance play crucial roles to establishing 

the link between suspected terrorists and funding sources and front companies throughout the 

region. Indonesia’s establishment of the Financial Transaction and Report Analysis Centre 

(PPATK) proved pivotal in the advancement of CT intelligence in recent years. Dismantling the 

funding and support structures for JI have remained a top priority for all intelligence agencies in 

recent years and have led to significant arrests vastly reducing JIs ability to conduct operations. 

INTERNATIONAL INTELLIGENCE SUPPORT 

Indonesia has become a significant participant in several regional and international initiatives 

that lend to increased counterterrorism support from the international community. Additionally, 

countries such as the United States, Australia and Malaysia have recognized terrorist groups such 

as JI as significant threats to national security and instituted measures that coincide with 

Indonesia’s increased security apparatus. Main initiatives include the Asia-Pacific Economic 

Cooperation (APEC), The Association of Southeast Asian Nations (ASEAN), and ASEAN 

Regional Forum (ARF)112. 

The United States recognizes not only JI but other militant Islamic groups in Southeast Asia as a 

significant threat to its national security. The US has sent significantly increased intelligence 

assistance to Indonesia and has sent members of the Central Intelligence Agency, Federal Bureau 

of Investigations, the National Security Agency, and Departments of Justice, Homeland Security, 

Treasury, and the Alcohol, Tobacco, and Firearms to Indonesia to assist in investigations into 

terrorist activities. The primary focus of US CT assistance is Counter Narco-Terrorism (CNT), 

terrorist transit, and the financial transactions of transnational terrorists113. The US also provided 

Indonesia significant assistance through the US Anti-terrorism Assistance (ATA) Program. This 

congressionally funded program is sponsored by the US Diplomatic Security (DS) service. The 

ATA program trains civilian security and law enforcement personnel from friendly governments 

in police procedures that deal with terrorism. DS officers work with Indonesia and a team from 

the US mission to develop the most effective means of training for bomb detection, crime scene 

investigation, airport and building security, maritime protections, and VIP protection114. 

The Australian Secret Intelligence Service (ASIS) and the Australian Security Intelligence 

Organization (ASIO) also recognize JI as a direct threat to the safety of its citizens and provides 

assistance to BIN in the form of information sharing and collection. The ASIO is also 

responsible for monitoring the movement of transnational terrorists in and around Australia and 

coordinates closely with the Indonesian, US, and regional governments115. The attacks on the 

Australian Embassy in 2004 and the second Bali attack in 2005 resulted in a significant increase 

in cooperation between Indonesian and Australian intelligence agencies with the intended goal of 

dismantling JIs network. 

The Malaysian government made a significant stride toward regional cooperation with the 

establishment of the Southeast Asia Regional Centre for Counter-Terrorism (SEARCCT). The 

 

112 Ibid. pg 63 113 OSINT - See ASIS.gov.au for further information 114 For more information on the ATA, see www.state.gov/m/ds/terrorism/c8583.htm 115 OSINT – See ASIO Corporate Plan 2007-2011 www.asio.gov.au 

35 
SEARCCT was established in November 2002 under the purview of the Ministry of Foreign 

Affairs as a regional CT centre focusing primarily on training, capacity-building and public 

awareness programs. The Centre was officially launched on 1 July 2003 and is located in Kuala 

Lumpur116. To date, more than 20 countries have taken part in information sharing and CT 

courses designed to increase the proficiency of host nation CT forces. 

Additional CT intelligence cooperation exists between Indonesia the governments of Singapore, 

Thailand, Philippines, and Japan. Each step toward a collective CT intelligence apparatus vastly 

reduces the capabilities of groups like JI. 

MILITARY COUNTERTERRORISM 

Indonesia has always recognized the importance of a CT force due to its proximity and 

dependence of the Straits of Malacca and large amounts of oil and natural gas. These targets 

provide terrorists a significant opportunity to strike at Indonesia’s fragile economy and disrupt 

the government’s effectiveness. 

Within the TNI, Indonesia established the Kopassus or Special Forces Command in 1985117. 

Kopassus was organized into four operational or strike battalions of 72 men 

each. Group 1 consisted of two battalions stationed on west Java and would 

accomplish Unconventional Warfare (UW) operations for western Indonesia. 

Group 2 consisted on the other two battalions and was stationed on Solo. 

Group 2 would be responsible for UW operations for eastern Indonesia. From 

the beginning, Kopassus has been modeled after the British Special Air Service 

(SAS) and ready to perform a wide range of SOF operations. Group 3 would 

become the training group for new recruits and provide a pipeline for 

Indonesian SOF118. 

 Source: specialoperations.com 

In addition to the Groups 1 and 2, Kopassus also contains the CT unit Detachment 81. 

Detachment 81 was a significantly smaller unit with the single mission of CT119. US SOF teams 

 

116 Malaysian Ministry of Foreign Affairs press statement 117 Indonesian Special Forces had existed since 1950, but Kopassus was the first unit aligned under modern SOF 

organization. See Conboy, Ken. “Kopassus; Inside Indonesia’s Special Forces” 2003 pg 306-315 118 Kopassus grew to 3 battalions in each group by 2005. 

36 
played a significant role through the late 1980s and early 1990s in the continued development of 

Detachment 81. In 1992, the International Military Education Training (IMET) program was 

suspended in Indonesia. This suspension ended US SOF training with Kopassus and Detachment 

81120. This lack of interaction occurred during the meteoric rise of JIs organizational 

operations121. British and Australian SOF have trained with Detachment 81 and served in an 

advisory role during the East Timor conflicts in 1995. Following the attacks on 9/11, the Bush 

administration argued to Congress that the suspension of aid to Indonesia impeded the War on 

Terror in Southeast Asia. A solution was reached with the US Regional Defense CT Fellowship 

(RDCF) program. The US used the RDCF to “earmark” $3.9 Million for Indonesian CT 

training122 and lines of communication are slowly being reopened. 

In addition to the POLRI intelligence arm, the National Police created Detachment 88 in 2003. 

Its creation was spawned from the Bali bombings in 2002123. This special unit is within the 

POLRI is funded by the US through the Diplomatic Security Service. The unit is located 30 

miles south of Jakarta. Ironically, the majority of Detachment 

88’s instructors were former US SOF. Detachment 88 is 

designed as a domestic CT unit that is capable addressing a wide 

range of activities, from bomb threats to hostage situations. This 

400-person strong special force was fully operational in 2005. 

The organization consists of investigators, EOD, an assault unit, 

and a sniper element124. 

COUNTERTERRORISM STRATEGY FOR TOMORROW 

Counterterrorism (CT) is often thought of as a military issue. This is a faulty assumption as 

terrorism is, first and foremost, a political act. CT strategy must therefore be a political 

countermeasure using all facets of the instruments of national power. In Indonesia’s case, they 

have made tremendous progress toward goal since the Bali bombings in 2002. Indonesia must 

continue to make progress in five key areas: legitimize the government, economic development, 

religious tolerance, further develop intelligence resources, and evolve military and national 

police capabilities and interoperability. These fundamental areas strike at the heart of 

Indonesia’s ability to thwart future terrorist development. 

GOVERNMENTAL LEGITIMACY 

Indonesia endured 33 years on authoritarian rule under Suharto. The centralization of every 

function of the government and military prevented terrorist expansion often at the expense of 

human rights and legal norms. When Suharto fell in 1998, the rapid decentralization of the 

government came at the expense of legitimacy. Indonesia had four different presidents in the six 

 119 Ibid 313-315 120 An amendment to the Foreign Operations Appropriations Act in 1992 suspended all military sales and training to 

Indonesia in response to human right violations by the TNI in East Timor. 

121 The cancellation of IMET was another antecedent mentioned in the preface that, individually, did not impact JI 

but when put together with all of the other factors within the Indonesian military created a root cause behind the 

inability to stop JI before they began operations in 2000. 122 Wise, William. “Indonesia’s War on Terror” Aug 05. United States-Indonesia Society pg 70-71 123 The number chosen for Detachment 88 comes from the largest number of casualties from any country as a result 

of the Bali bombings. Australia lost 88 citizens in Bali. 

124 http://en.wikipedia.org/wiki/Detachment_88 

37 
years following Suharto125. While a testament to democratic reforms, each president vectored 

Indonesia in a different direction and lacked the support for significant progress. Another factor 

in the decentralization process was the lack of true candidates at the local, regional and national 

levels of government. The removal of the military (TNI) from the national ruling body also 

played a role in the loss of true progress. These dramatic reforms weakened the presidency, 

national and local governments, and the military and allowed militant Islam to flourish in its 

wake. As the government continues to evolve, Indonesia must continue to stride toward 

establishing all levels as legitimate bodies of law. Addressing the societal woes of Indonesia’s 

disenfranchised groups is paramount to the long term stability of the country. At the local level 

of government, politicians must begin the process of establishing legitimacy by addressing 

societal concerns and identifying root causes of strife. All of these factors are absolutely 

paramount to legitimizing Indonesia’s political process. 

ECONOMICS AND RELIGION 

The 1997-1998 Asian financial crisis wreaked havoc on Indonesia’s fragile economy. Indonesia 

lost 13.5% of its Gross Domestic Product (GDP) in 1998126. The result of this downturn was 

nearly 10% of Indonesians unemployed. Unemployment bred discontent and this defined one of 

the core antecedents addressed in this paper. Indonesia has slowly recovered but there is much 

to be done. The economic aspect of this paper is directly linked to legitimizing the government. 

All politicians, from local to national, must carefully examine economic factors from rural 

villages to the sprawling metropolis of Jakarta. The terrorist recruitment cycle feeds on the poor 

and attracts potential recruits with money and an identity127. Terrorist organizations are quick to 

recognize attractive recruitment areas and often send charity and relief organizations in as part of 

a conditioning phase. This is used to gain popular support which translates to recruitment and 

protection during the transit of operatives. By addressing these economic factors, governments 

can reverse the equation and delegitimize terrorist organizations by gaining the support of the 

local populace. Economic development is a critical factor in stability and paramount to an 

effective CT strategy. 

On the other end of economic spectrum, Indonesia must continue to develop the capacity to track 

the financial transactions of JI and terrorist groups. In the US, most organized crime trials center 

on illegal financial transactions. This avenue is critical to both the development of intelligence 

agencies and to legitimizing the government. International cooperation is also a vital link to this 

process. 

Indonesia is the fourth most populous country in the world and nearly 86% Muslim128. Under 

Suharto’s regime, The Muslim United Development Party (PPP) was discouraged from playing 

an overly active role in introducing religion into the Pancasila129. When Suharto fell, extremist 

Muslim group across the archipelago raced to the political forefront. This caused significant 

turmoil within the Christian and Buddhist minorities. While Indonesians are overwhelmingly 

 

125 Presidents Habibie was given a no confidence vote after just 18 months in office, Wahid was impeached just 

under 2 years in office, (Mega) Sukarnoputri was the daughter of Sukarno and Indonesia’s first female president, 

and finally Yudhoyono who was sworn into office in 2004. 

126 http://en.wikipedia.org/wiki/Asian_financial_crisis 127 It is important to note that most terrorists from Indonesia were middle class men with decent jobs. This concept 

addresses one facet of recruitment and local support for terrorist operations. 128 Library of Congress, Indonesia; a Country Study. 1993 http://countrystudies.us/indonesia 

129 Ibid; http://countrystudies.us/indonesia/86.htm. Pancasila insisted on a culturally neutral identity and nationalism 

expressed in the unity of Indonesia. It did not recognize Islam as the only religion. 

38 
moderate Muslims as a whole, extremist and militant groups have been able to flourish since 

1998. A weak central government and high unemployment following the Asian financial crisis 

paved the way for groups like JI to actively campaign for new recruits. The intricate relationship 

between religion and government is especially important. Indonesia’s CT strategy must balance 

the Islamic teachings in the Pondok and the rise of political parties like the Justice and Prosperity 

Party130 with the increasing paranoia and vigilantism of Indonesia’s Christian minority. 

Indonesia must continue to make a concerted effort to promote dialogue and a peaceful 

coexistence between the Muslim and Christian population. Intelligence, economics, and 

government are distinctly linked to the issue of religion and CT. 

An effective CT strategy must segregate Indonesia’s moderate 

Muslims from the radical fringe consisting of Salafi and Wahhabi 

Jihadists. Understanding the Muslim ring of faith is imperative 

when attempting to differentiate actual grievances from terrorist 

ambitions. If the goal of the jihadist is to establish a pan-Asian 

super-state and ultimately join the Islamic Caliphate, steal the 

argument. The objective of an effective CT strategy is not to deny 

Muslim pride but to celebrate its achievements other than Jihad. 

Islam spread more rapidly during the original Islamic Caliphate by 

merchants and education than by the sword. Showcase Muslim 

scholars and their achievements like algebra and the advancement of astronomy131. Breaking the 

link between religion and militant Islam is an essential element to changing the view of Islam 

throughout the world. 

Economics and religion worked in tandem for the Caliphate throughout its history. CT strategy 

should compare the differences between modern day Dubai, United Arab Emirates and the caves 

that house AQ or the safe houses that harbor JI fugitives. Continue to highlight the Muslims that 

were killed during the Christmas Eve church bombings and in Bali. Which ideology is doing 

more to advance the greatness of the Islamic world? AQs brand of Salafi-Wahhabi jihad proved 

capable of destroying great works in the Muslim world and the West. In many ways, Dubai 

resembles the actual Caliphate far more than any Shariagoverned village. While JI is having enormous difficulty 

expanding its base, the United Arab Emirates can soon boast of 

the world’s tallest building and is a destination of investors, 

scholars, and Muslims from around the world. All of this was 

accomplished without jihad. So the argument starts there: the 

moderation of Islam based on economics, infrastructure and 

scholarship leads to greatness witho 132 ut compromise . 

 

130 Perlez, Jane; “Spread on Islamic Law in Indonesia Takes its Toll on Women” 27 Jun 06 The New York Times. 

Accessed on 1 Mar 08. http://www.nytimes.com/2006/06/27/world/asia/27indo.html 

131 Muhammed ibn masa al-Khwarizma was a Muslim scholar credited with significant advancements in the fields of 

mathematics and astronomy. He spent much of his life teaching at the House of Wisdom in Baghdad, Iraq. See 

http://www.algebra.com/algebra/about/history/Al-Khwarizmi.wikipedia for more information. 132 This paragraph is based on discussions with David Blair concerning moderation of Islam. 

39 
INTELLIGENCE REFORM 

Everything begins and ends with intelligence. While Indonesia’s State Intelligence Service 

(BIN) has undergone significant advancements in recent years, there is still much to be done. 

BIN agents must establish a much better human intelligence (HUMINT) network in order to tie a 

multitude of antecedent clues together. This is accomplished by working much more closely 

with local levels of government and growing in size and capacity. BIN’s current focus on 

internal threats should continue to evolve with emphasis on how they relate to external factors 

such as foreign jihadists and financing. Additional emphasis on mapping (GEOINT) and signals 

(SIGINT) intelligence will aid in intelligence driven future 

operations against militants. This is a very brief examination 

into the CT portion of BINs capability that is part of a much 

larger intelligence apparatus. The concept behind the 

intelligence portion of Indonesia’s CT strategy should be to 

isolate JI and other militant groups from external influences 

followed by insulating particular groups from each other and 

finishing by map tracking and development of potential terrorist suspects. All of this should be 

done in coordination with the TNI (BAIS) and the national police (POLRI) intelligence services. 

Operational security and the methods of collection are important aspects of BINs work and it is 

understandable that there is a reluctance to share sensitive information but not at the expense of 

an effective CT campaign. 

MILITARY, LAW ENFORCEMENT AND THE WEST; IRREGULAR WARFARE 101 

Finally, with the decentralization of the government in 1998 Indonesia’s military (TNI) and 

National Police were split into two organizations. Critical information on terrorist suspects was 

fragmented or lost during the segregation. The ensuing four years of infighting and stove piped 

information allowed JI to evolve into the organization that it became. Following the Bali 

bombings in 2002, Indonesia has made tremendous strides in both the TNI and the National 

Police cooperation in terms of CT. Both agencies were instrumental in the apprehension of key 

JI members. This continued cooperation between both units is imperative to the continued 

success of the CT campaign. 

The way ahead is difficult to predict. CT is just one piece of the larger solution. The US and 

the West view violent extremism and militant Islam and a direct threat to National Security and 

should help with strengthening Indonesia’s ability to counter terrorist groups before they can 

develop into the threat JI was able to exhibit. This can be accomplished by employing all five 

pillars of Irregular Warfare (IW). 

Irregular Warfare is defined as a violent struggle between state and non-state actors for 

legitimacy and influence over the relevant population.133 As we peel back the layers of IW 

FID is an important piece of the larger IW strategy. As the saying goes, an ounce of prevention 

is worth a pound of cure. Due to exchange rates, macroeconomics and the mechanics of guerilla 

warfare, a terrorist group like JI will consistently experience 

positive spending multipliers against the government. A reactive 

strategy to JIs attacks will only increase those multipliers. One 

dollar spent by JI may cost the government, whether Indonesia or 

the US, a thousand dollars in active stabilization, but ten dollars 

 

133 Irregular Warfare Joint Operating Concept version 1.0, 10 May 07 

40 
worth of preemptive stabilization could have rendered that one dollar impotent. Posturing 

Indonesia against JI and future terror incursions will nearly always be cheaper and often more 

effective than reacting to JIs acts of terrorism. 

The US Department of State is normally the lead agency for FID operations134. Traditionally, 

FID has always been geared toward COIN operations. With the emergence of JI and the Global 

Jihad, more emphasis should be placed on the internal development portion of FID to prevent 

those insurgencies before they arise. In the case of Indonesia, this involves a three-pronged 

approach. First, the US and the West must assist in strengthening the TNI and National Police 

capabilities. Integral training and development should continue from the Departments of 

Defense and Homeland Security as well as the Department of State. The US military supports 

this concept through the Joint Combined Exchange Training (JCET) program135; the Department 

of Homeland Defense can support this concept through the development of Indonesian Fusion 

Centers136, and the ATA program from the Department of State. Each of these programs offers a 

significant increase in Indonesia’s ability to identify and counter JI operations. The second 

portion of FID is Humanitarian and Civic Assistance (HCA) operations. Repairing a well or 

immunizing a village against diseases is an important step in gaining support from the local 

population. If the locals support the government, they are less likely to provide safe harbor to 

terrorist organizations such as JI. This is a fundamental concept in the “ounce of prevention” 

strategy and cannot be a one-time “good deal”. HCA should be an ongoing operation designed 

to both gain support and establish presence across Indonesia’s 27,000 island archipelago. If 

HCA is initiated by the US, Indonesians can continue the operation with US assistance. The 

third piece of FID is equipment under the Foreign Military Sales (FMS) program. With an 

increased presence through HCA and increased police and military capability through JCETs and 

the ATA program, Indonesia will require additional equipment to increase their ability to 

successfully counter JI. 

 

134 Joint Publication 3-07.1; Joint Tactics, Techniques, and Procedures for Foreign Internal Defense (FID) 30 Apr 

04. Pg 34 

135 JCET programs are exercises designed to provide training opportunities for American SOF by holding the 

training exercises in countries that the forces may one day have to operate in, as well as providing training 

opportunities for the armed forces of the host countries.

136 In the US State and local authorities have created 38 Fusion Centers around the country. Fusion Centers blend 

relevant law enforcement and intelligence information analysis and coordinate security measures in order to reduce 

threats in local communities. See http://www.dhs.gov/xinfoshare/programs/gc_1156877184684.shtm for more 

information. 

41 
In areas where JI has control or support of the local population, the government must examine 

the fundamental ends, scope, and core grievances of the population. During the clear phase, 

brief offensive operations may be effective in isolating core members of JI from the population. 

The increased capability of the TNI (BAIS, Kopassus-Detachment 81) and the National Police 

(POLRI and Detachment 88), working in concert with BIN and international intelligence 

communities, would allow the COIN force to engage in previously denied areas. The operation 

should be limited in scope to apprehending JI or terrorist elements and setting the conditions for 

FID/HCA operations in the area. The process is cyclic and continual. 

The CT continuum is not complete without Information Operations (IO). IO is present in every 

facet of CT strategy and critically important in this phase. The instruments of power work hand 

in hand to effectively counter JI and terrorists in Indonesia. Terrorism is like a spider web; it 

cannot be destroyed unless it is attacked at its anchor points. COIN attacks the inner portions of 

the web but does not address the roots causes that lead a group like JI to attack. FID addresses 

Indonesia’s CT capability and IO continuously engages the anchor points, those antecedents that 

led to the creation of JI. If the environment favors the enemy, identify those anchor points that 

allow him to flourish. By changing the environment, the probability of success is increased. 

CONCLUSION; THE BALI PARADOX

The fundamental aspect of any CT strategy is to prevent terrorist groups such as Jemaah 

Islamiyah from committing terrorist acts. Indonesia, a country defined by struggle and conflict, 

is often reluctant to modify its CT strategy designed to prevent terrorist acts yet evolves after a 

significant terrorist act occurs. Until Indonesia recognizes the paradox, they will be forever part 

of it... 

42 
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