Basilio Araujo is subdued. Over breakfast in a modest hotel in south Jakarta, the former spokesman of the East Timorese pro-integration forces is less than his usual talkative self as he contemplates the future for the defeated militias.

It is a long way from how things used to be. The former East Timorese civil servant, who studied psychology at Manchester Polytechnic on a British Council scholarship, has lost his authority.

Attempting to explain away the violence, murder and destruction visited on East Timor by the militias, the one-time spin-doctor and intellectual face of the integration movement is sounding worn and tired.

The arguments are still there, but the privileges are gone. With Indonesia formally washing its hands of East Timor, the business-class tickets and five-star accommodation once provided by patrons in the Indonesian administration have disappeared.

Now the future is uncertain for East Timorese militia and integration leaders who have renamed themselves The Forum for National Unity.

Although many have been named as war criminals by international human rights organisations, they say they are determined to continue the struggle for integration with Indonesia in the newly-independent country.

"If [resistance movement] Fretilin can resist in the jungle for 23 years and they are Timorese, we are also Timorese and we also know our jungle and we know what our nature can provide us to eat, so we can also resist in the jungle," says Mr Araujo.

"For a person who might be listed as a war criminal, of course, they will choose to die in the battle rather than be humiliated."

These East Timorese will tell you their culture is based on violence. During the 400 years of Portuguese colonisation, the Portuguese backed local leaders in regular wars between clans and tribes.

"We are born heroes and we die warriors," says Mr Araujo, quoting an East Timorese saying which he uses to explain the outbreaks of militia violence before and after the referendum.

The militias trace their history to the beginning of Indonesian rule. When Indonesia invaded East Timor in 1975, a number of East Timorese supported the Indonesian army working as guides, porters and intelligence gatherers.

"Militia commanders say the militias already existed before 1998," said East Timorese human rights campaigner Aniceto Guterres in Dili in August. "The first time the militias were formed was to help the Indonesian military who didn't know what the ground was like in intelligence operations in the jungle."

These East Timorese were generously rewarded for their help, often with positions of power and influence.

But it was only after the United Nations-sponsored referendum was announced in January that distinct militia groups began to grow in force and take shape as an anti-independence movement, backed by elements within the Indonesian army which provided arms and training.

The link between militias and the Indonesian military has been well-documented. Indonesia's former foreign minister, Ali Alatas, admitted recently that the military was culpable in the violence that followed the vote for independence. Elite special forces (Kopassus) are known to have had a long involvement in the territory.

As early as November last year, according to reports by an Australian East Timorese support group, Kopassus agents were working undercover at a pro-independence rally near the East Timorese town of Alas.

The crowd at the rally discovered and killed two of them, leading to brutal reprisals by the army and the disappearance of several East Timorese youths.

"The military was making preparations ever since the incident in Alas," said Mr Gutteres. "At that time it created new militias such as the Mahidi [Live or Die for Integration] and Besi Merah Puti [Red and White Iron]. They were supplied with weapons by the military and they were also allowed to create new hand-made weapons."

Since their departure to West Timor following the arrival of international peacekeepers (Interfet), the strength and commitment of the defeated militia forces has been difficult to gauge.

Mr Araujo says there are 47,000 militiamen in West Timor and 5,000 still in East Timor waiting "to kill or be killed". Interfet has detained and disarmed an undisclosed number in East Timor, though it has no authority to charge them, and at least five have been killed in border skirmishes.

With training sessions on view to Indonesian television cameras in West Timor, militias say they are grouping in preparation for a possible attack on Interfet. Militia leader Joao Tavares boasts he has a force of 50,000 ready to strike across the border.

But according to East Timorese journalist Mehta Guterres, the number of hard-core devoted militiamen is much smaller. "The real hardliners are only about 5,000," he says. "They are the ones who have supported Indonesia forever, since the partisan days. They are old hands. There is no support among the young people. The rest are trying to save themselves as they will be killed if they don't remain in the militias."

In the past few weeks, a fresh battalion of troops from Sulawesi has been sent to the West Timorese border to disarm the militias.

However, in a visit last week to the West Timorese capital, Kupang, American ambassador Robert Gelbard said it was obvious some elements of the army were still supporting armed activity. Indonesian human rights group Kontras has reported that militias are openly operating under the watch of Indonesian police in refugee camps in Kupang and border town Atambua.

But this local level of support may not be enough to sustain the guerilla movement threatened by militia leaders in Jakarta. The Indonesian chain of command previously directing militia activity no longer exists.

Army and police commanders who operated in East Timor have moved on, in many cases rewarded for their work. Former regional commander General Adam Damiri has been promoted to assistant to the army chief on operational affairs. Former Dili chief of police, Colonel Timbul Silaen, is now brigadier-general of the police headquarters' anti-corruption force.

Over the next few weeks, the Forum for National Unity will decide whether to continue armed-resistance or work through political channels for a voice in the independent East Timor. Under the threat of a possible war crimes tribunal and lacking popular support in Indonesia, there is a feeling among the pro-integration forces that they have been abandoned.

"I think Indonesia owes us an apology because like Portugal, they have washed their hands as well," says Mr Araujo. "I think that was what they wanted to do because I think Indonesia does not want to be accused any more. Now everything is finished. Now they are gone, leaving the East Timorese alone."

The East Timorese who were drawn into militia organisations can be grouped into three distinct categories.

Of these the most prominent were those East Timorese who were already members of civilian security forces, operating alongside the Indonesian military and police to provide intelligence on independence activists and the Falintil guerilla army.

Among them were militia leaders like Eurico Guterres, formerly a small-time gambling boss in Dili who headed the group Aitarak (Thorn).

Although Mr Guterres claimed he was a people's leader who took orders from no one, he told journalists early this year that he answered directly to General Damiri.

For a small-time player, he had influential friends. Photographs found in his headquarters after international troops arrived in Dili show him with former president Suharto.

Then there were those recruited under pressure as the militias established themselves. Many were threatened with death or the burning of their houses if they did not join. In the period before the referendum, it was not unusual to find men who wore the uniform of the militias and attended mass rallies, but privately expressed their wish to vote for independence.

The third group was made up of thieves and thugs who saw opportunity in joining with the dominant military force. These people were amply rewarded in the three-week looting and burning spree that followed the result.

For months before the referendum, militia groups terrorised the population, threatening and killing pro-independence supporters. After the overwhelmingly pro-independence result was announced, militias took over the territory, backed and supported by the army.

It is not known how many died in the violence. Numbers have been estimated in the hundreds, rather than the thousands first feared. But every village, town and city in East Timor has a tale of horror to tell and more than a third of the population was forced across the border to be held in refugee camps in West Timor and around Indonesia.