The news that prominent researcher and whistle-blower Dr Sidney Jones of the International Crisis Group (ICG) has been served her marching orders from Indonesia should not strike Indonesian-watchers as surprising.

For Sidney Jones (photo right) has unearthed vital pieces of information - more so than any other researcher in the field to date - and her findings have ultimately proven to be embarrassing for the powers-that-be in Jakarta.

While not every scholar in the field may agree with all her conclusions, and some would argue that there has not been enough rigour and discrimination in her reading of the whole pesantren/madrasah (religious seminary) phenomenon in the country, it cannot be denied that she and her team at ICG were among the first to re-construct the complex network of individual actors and agents, families, business and educational contacts and marriage ties that make up the nebulous network of radical conservative Islamists in the country.

Whether or not the elusive underground movement summarily labelled 'Jama'ah Islamiyyah' actually exists in Indonesia and what its purported goals and aims may be remain an open question to most. But what has upset some sections of the Indonesian political and military elite are not the findings of Sidney Jones and her team, but rather the links and ties that they have also uncovered in the course of their research - not least to sections of the Indonesian military elite.

Here, then, lies the crux of the matter: Since September 11, 2001 and more importantly the Bali bombings that took place a year later, Indonesia has been roped into the so-called 'coalition of the willing' and has been seen and presented as a 'model Islamic state' by Washington while the latter was hell-bent on pursuing its interests in Afghanistan and Iraq. From being cast as a dysfunctional state tottering on the verge of collapse and financial ruin, Indonesia has been elevated to a major strategic and political ally of the West and the USA in particular. Along with Pakistan (another major non-NATO ally of Washington), Indonesia looms large in the political calculations of the hawks and neo-Cons of the White House who see it as a major player in the global war against so-called 'radical militant Islam'.

On 'wanted' list

With the turning of the political tide, Indonesia's military elite and security agencies have had a field day: From vilified pariahs they have suddenly been re-elevated to the status of saviours and defenders of the Indonesian state - a dubious promotion to say the least, considering their role in numerous cases of human rights abuses in troubled regions and provinces like Aceh, South Sumatra, West Irian and East Timor. During the peak of the reformasi (reform) movement in 1998, many of the senior leaders of the Indonesian army and intelligence services were accused of torture and murder, and most of them were seen as wanted men. Today they remain on the 'wanted' list, but wanted by Washington instead.

A case in point would be ex-General AM Hendropriyono, who was a household name in Indonesia but for all the wrong reasons. During the Soeharto era he was one of the key generals who ran the Indonesian army's intelligence and counter-insurgency apparatus, and under his guidance the Indonesian special forces and covert ops units were responsible for some of the worst human rights violations in Indonesia's history. It was he who was put in charge of the operations in the Lampung district in South Sumatra, where the Indonesian army was given the task of 'containing' the 'threat' of Islamist activists and mass movements there.

Hendropriyono's actions were typical of the man: after a series of covert actions and psy-op warfare (where the public was told that the Islamists were a 'terrorist threat') the army was ordered to move in for the kill. The end result was the massacre of hundreds of innocent civilians, and this earned Hendropriyono the nickname 'the Butcher of Lampung'.

Rather than have the man taken to court, Hendropriyono has been made the head of Indonesia's new counter-insurgency intelligence service instead! Likewise ex-General Wiranto (left), who has been accused of all manner of human rights abuses in East Timor, is now brazen enough to think that he can run for the post of President of Indonesia.

The most worrying development of all has been the near-total erasure and collective amnesia about the close links between the Indonesian army, intelligence and the so-called 'Islamic militant groups' in Indonesia themselves. When the Indonesian government was told to rein in these groups some of their leaders - such as Jaafar Omar Thalib, leader of the infamous 'Laskar Jihad' militia, openly stated that they enjoyed close relations with the Indonesian army.

And these links go way back to the sordid past of Indonesia when it was under the helm of President Soeharto (right). One such bogus 'Islamist militia' was the shadowy Komando Jihad group that emerged in Indonesia in 1977 and was under the leadership of the young Indonesian cleric Imran bin Zein. An underground paramilitary movement, it was based mainly in Jakarta and Bandung, West Java, and its members were mainly young disaffected Muslims from the cities. After the Iranian revolution of 1979, however, the leaders of the Komando Jihad claimed that they would embark on a revolutionary struggle against the Indonesian state. By then it was widely speculated that the Komando Jihad had actually been set up under the watchful eye of Indonesian army intelligence, who wanted to use the Komando Jihad to eliminate opponents of the government and residual elements of the banned Communist party of Indonesia.

Beyond purely symbolic

Later in the late 1990s groups like Jaafar Omar Thalib's Laskar Jihad came on the scene and made the headlines with their 'moral cleansing' campaigns that often involved violent raids on hotels and bars in the country. But it should also be noted that groups like the Laskar Jihad, Fron Pembela Islam and Majlis Mujahideen Indonesia also played a role in creating havoc in troubled regions like the Moluccas, which in turn served as the pretext for further military intervention there, as well as in other places like Timor and Aceh.

Taking into consideration these factors and the complex and murky history of Indonesia's army and intelligence services, it should come as a surprise if Sidney Jones and her research team at ICG discovered concrete evidence of ties that go beyond the purely symbolic. It also explains why she and her researchers have become an embarrassment for the Indonesian government and why they have been told to pack their bags and keep their mouths shut. As Indonesia blunders its way towards another presidential election, the stakes have risen accordingly: With the army poised to stage a comeback and the economy still on the verge of collapse, the skeletons of the past have been hurriedly buried once again while the criminals allowed to run free.

Dr FARISH A NOOR is a Malaysian political scientist and human rights activist. His 'The Other Malaysia' column appears in malaysiakini .