What role should Islam play in Indonesia? The question is central to the future of the country, but its origins are steeped in history.
Intelligence agencies are convinced Abu Bakar Bashir is central to Jemaah Islamiah
Islam was first imported to Indonesia by traders from the Middle East and South Asia some 500 years ago.
But it developed a more political focus during Indonesia's struggle for independence from Dutch colonial rule.
In 1945, Muslim political leaders failed to get Islamic, or Sharia, law enshrined in the newly independent country's constitution.
To this day, Indonesia remains a secular state and the vast majority of its citizens wish it to stay that way, in spite of the fact that more than 80% of the population describe themselves as Muslim.
But a small, and in some cases influential number of Indonesians have never given up on the dream of an Islamic state. Some have been prepared to resort to violence in pursuit of their aim.
The roots of radical Islam in Indonesia can be traced back to a movement called Darul Islam, literally "abode of Islam". Darul Islam was established in the late 1940s to fight politically and physically for an Islamic state, based on Sharia law.
The movement suffered a major setback under the authoritarian leadership of former President Suharto, who, having once courted Islamists as a useful counterweight to the power of the military, turned against them in the mid 1980s.
The crackdown was bloody and brutal. Many Islamic leaders ended up in jail or fled into exile, among them Abu Bakar Bashir, a radical cleric who earlier this month was found guilty of sedition by a Jakarta court.
The prosecution had also accused Abu Bakar Bashir of being the spiritual leader of a militant Islamic organisation called Jemaah Islamiah but the judges ruled there wasn't enough evidence to prove it.
Nevertheless, regional and western intelligence agencies remain convinced that Abu Bakar Bashir is a central figure in the network which they say he co-founded while in exile in Malaysia.
Abu Bakar Bashir returned to Indonesia after the fall of Suharto in 1998. His hardline views were tolerated and he was able to continue teaching at his boarding school in central Java.
The new democratic government of Indonesia was unwilling to take any action which might appear similar to the repressive tactics employed by Suharto.
But the Bali bombings in October last year, transformed the political landscape. More than 200 people died in the blasts, mostly foreign tourists.
For months foreign governments had been warning of the possibility of an attack by Islamic militants, but before Bali, President Megawati, had been reluctant to act, fearing a Muslim backlash.
More than 200 people died in the Bali bombings
After all various Islamic oriented parties together attracted about 35% of the vote at the last election. After Bali, however, the climate changed.
Around 90 suspected members of Jemaah Islamiah have been arrested and more than 30 have been charged in connection with the Bali bombings.
The evidence given by those who have already been put on trial has confirmed the existence of an extremist Islamic network whose members are determined to use any means to achieve their aim of establishing a "pure" Islamic state in Indonesia.
Many of the key suspects are graduates of Abu Bakar Bashir's school and veterans of the fight against the Soviets in Afghanistan.
Guide: Militant Islamic groups
Profiles of the main Islamic militant groups around the world.
Many more volunteered to fight Jihad, or holy war, closer to home, fuelling the religious conflicts in Sulawesi and the Moluccas which have marked the past decade in Indonesia.
The vast majority of Indonesians have been appalled by what happened in Bali last year, and by the religious violence which has dogged the country for decades.
Most now accept that there is a small, but dedicated number of Islamic extremists within Indonesia who represent a serious threat to the country's security.
But some senior Muslim leaders, even those from the major moderate Muslim groups, continue to put forward the view that some foreign power must have been involved in the Bali plot.
There is a battle being waged for the soul of Indonesia
They criticise the media for being too quick to blame terrorist attacks on Muslim extremists. Such denial is worrying for the future of the country.
The majority of Indonesia's 220 million citizens define themselves as Muslims and most practice a liberal, tolerant version of their religion.
They would like that moderate interpretation of Islam to be defended by their leaders, both political and religious.
There is a battle being waged for the soul of Indonesia. A battle between conservatives and liberals; between modernisers and traditionalists.
It's not just about the place of Islam within Indonesia. It's about what kind of country Indonesia wants to be.
This article is partly right. However, please note that historically Muslim fundamentalism has never been popular in Indonesia. There are no Wahhabis here. I agree that the Bali bomb was shocking. The way out is for us to find out why those bombers were so misguided that they followed that course to ensure that this does not happen again.
I am suspicious of how the 'modern' applied. Does the term 'modern Muslims' refer to those who follow the ideologies of Western countries? And what should we be calling those who choose, by their free will, to practice Sharia Law? Will they be regarded as being against the so called "modern world"!
Aburaas Bashir, Goldogob, Somalia
Your article is very interesting. For me, the title of the piece didn't represent the Indonesian Muslim people. You only mention Abu Bakar Ba'ashier's story but Indonesia has many well known, intelligent and moderate clerics.
"They would like that moderate interpretation of Islam to be defended by their leaders". This suggests that it is not being so defended. Certainly, the voice of moderate and politically and intellectually creative Islam is not easily heard above the cries of dismay. Would you say something about any coherent liberal Islamic movement emerging in this part of the world?
Elizabeth Abbott, Australia
As a Muslim I find it very disheartening that in order to represent Islam some people are using ways which are totally prohibited by Islam.
Farhan, South Korea