John McBeth, Jakarta – The flyer from the East Timor Pro-Integration Information Centre billed it as an "Invade Dili" rally. Three days later, on April 17, provincial governor Abilio Jose Osorio Soares and civilian and military officials looked on as militia leader Eurico Guterres told several thousand followers: "As from today, I order all the pro-integration militia to conduct a cleansing of the traitors of integration. Capture them and kill them."

With that chilling order – echoing another conflict in far-off Kosovo – the militia peeled off and began an unimpeded rampage through East Timor's provincial capital. Over the next two days they killed as many as 30 people and wrecked businesses and homes.

For many observers, the carnage confirmed suspicions that the Indonesian military is dead-set against President B.J. Habibie's offer to give East Timor independence if it rejects an autonomy proposal. It also added credibility to expectations that the autonomy plan, now being discussed at United Nations-sponsored talks in New York, will be significantly watered down. The result, analysts say, can only be a bloodier confrontation between separatists and integrationists among East Timor's 800,000 population.

Initially, Western officials and human-rights groups blamed rogue local commanders for opposing Habibie's independence plan. Now, however, they're convinced that while armed-forces commander Gen. Wiranto and the Jakarta military leadership may not have directly ordered the army to turn loose the militias, they tacitly allowed it – out of fear that independence will cause a ripple effect that could dismember the entire nation. The result has been the worst violence in East Timor since the 1991 Dili massacre.

"All circumstantial evidence points to Wiranto and the rest of the military leadership being overtly supportive of the pro-integration militia," says a Western military official. "They think Habibie is making a big mistake. They fear that if East Timor becomes independent, they'll be fighting independence movements in Irian Jaya and Aceh and even other places. They think it will just be opening the door." While most of the blame has been heaped on the military, diplomats note that since the original autonomy package was unveiled in June last year, separatist guerrillas have also been conducting a campaign of intimidation.

Diplomats have been sharply critical of jailed pro-independence leader Jose "Xanana" Gusmao for issuing a call to arms on April 5 that gave pro-integration paramilitaries the pretext to go on the offensive. Although Gusmao later tried to explain that he meant his followers should only defend themselves, the statement set in motion a chain of events that culminated in a massacre the next day at Liquica, 30 kilometres west of Dili. In the attack, pro-integration paramilitaries and Timorese soldiers shot and hacked to death 57 people in a churchyard.

Having originally denied that it was supplying weapons to the militia, the military is now making no secret of its support. During a meeting with visiting US Assistant Secretary of State Stanley Roth on April 14, Wiranto offered few regrets for the Liquica incident and said disarming the pro-integration militia will depend on Gusmao's Fretilin guerrillas turning in their weapons as well. His assertion, backed by little or no evidence, was that the integrationists had been provoked into retaliation.

Gusmao claims that senior regional military officers met Guterres and other militia leaders in Bali in March to form a 2,000-strong pro-integration front. "I think there's quite a lot to that," says a Western diplomat. "It doesn't matter what the high command is saying. At the sharp end, they're not supporting government policy."

Timorese and Western sources point out that one of the regional commanders currently responsible for East Timor is Brig.-Gen. Mahidin Simbolan, who captured Gusmao in 1992. Simbolan was head of intelligence for the Indonesian special forces before being appointed Dili commander in 1995-96.

But how much the military is actually running things is still a point of debate. Analysts note that after years of helping and doing business with the army, militia leaders would be vulnerable to retribution under independence. "Why should they be passive when the military shares their attitude and gives them support," says a senior Western diplomat. "I don't see them being under military discipline, but that doesn't relieve the military of responsibility."

Arming the militia, another Western official points out, is the military's way of "levelling the playing field," given the perception that the international community is fully behind the charismatic Gusmao, who was recently moved from Jakarta's Cipinang Prison to a special detention house.

But analysts can't determine whether the strategy is to sabotage the ballot altogether, or to intimidate the East Timorese in a way that heads off a lopsided vote in favour of independence.

The ultimate decision on East Timor's fate rests with the People's Consultative Assembly, Indonesia's highest legislative body. Depending on how the "consultation" is carried out, diplomats say the assembly is unlikely to cut East Timor loose from the republic if there's no more than a 60:40 vote for independence. As one put it: "The military appears to be following the logic that if there's not an overwhelming mandate for independence, then the government will feel justified in going with the autonomy package."

If East Timor is a pebble in Indonesia's shoe, the last seven weeks have shown why. While it initially appeared the military supported Habibie's independence offer, internal documents shown to the Review at the time the new policy was announced indicated Wiranto and the five other political and security ministers had wanted more time to study the proposal. They weren't given it, and two days later, the president made it official. From then on, the situation on the ground began to deteriorate.

Insiders familiar with the sequence of events say the military became aware Habibie was shifting his position on independence as early as December.

This may explain why two of the new militias – the Besi Merah Puti and Mahidi – were formed a month before the policy was announced. As with many of the 10 or more other pro-integration militias that sprouted in the weeks following Habibie's bombshell, both were raised in western East Timor, where pro-integration sentiment are stronger.

A month after Habibie's statement, the government began to backtrack on the autonomy package. At a cabinet meeting on March 8, government and diplomatic sources say, key ministers protested over the way Indonesia would have to continue subsidizing East Timor when, under an internationally guaranteed "special status" agreement, the territory would have far more freedoms than those being offered to 26 other provinces.

Serious concern was also expressed at the effect East Timor's independence might have elsewhere.

The president may have even begun to harbour second thoughts himself after a rowdy meeting with Irian Jaya leaders in late February, which showed just how high expectations had been raised by the East Timor initiative. The president was shocked and angered when some Irianese openly called for independence. Dispensing with his prepared remarks, he told them: "I'm not offering independence, I'm offering autonomy."

Foreign Ministry officials won't say which parts of the autonomy plan have changed, but they insist that a key provision removing the military from internal-security duties remains. "It has been watered down, but it's still a wide-ranging special autonomy," says an official familiar with the revisions. The changes are thought to centre on finance, the judiciary and foreign investment. "The concern is that while it has to be special, it shouldn't be to the extent where it poses a problem to our national interest," the official adds.

The question now, however, is whether a consultation process can be held at all. "Everyone is very worried," says a Western ambassador. "You can't have a free and fair process in an atmosphere when armed groups are running around." East Timorese legislator Salvador Soares agrees: "After what has happened, everything has changed drastically. The pro-integrationist forces now think they're on top. It's not the time to hold a ballot."

[On April 26, Lusa reported that an East Timorese guerrilla commander has died on April 17 from wounds suffered in an attack against an Indonesian military convoy near Laclubar. Commander Xerife, of the Falintil guerrillas' 3rd military region, Laclubar. Lusa said the guerrillas claim they destroyed five army trucks and seized weapons, including a machinegun, in the attack, which killed the brother of Indonesia's roving ambassador for East Timor - James Balowski.]