Killer militias organized by elements of Indonesia's army have murdered hundreds of East Timorese civilians and forced thousands more into exile. There is much talk of United Nations intervention and what form it should take. But the more important question behind the brutal local campaign is who will control Indonesia -- and what kind of Indonesia the world can live with.

The fall of Indonesian dictator Suharto in May 1998 seemed to promise the end of his "New Order" -- the ruthless suppression of a diverse nation by the army, motivated by a spoils system, with the lion's share of the spoils going to Suharto's family.

The new president, B.J. Habibie, a civilian, took steps (including holding parliamentary elections) to move toward civilian rule. A key signal was the departure of Gen. Prabowo, one of the Army's leading strongmen and Suharto's son-in-law. Prabowo was forced to resign and go into exile after an investigation showed that elements of his former Special Forces command, Kopassus, had been involved in the torture and "disappearances" of civilians.

Perhaps Habibie's clearest break with the "New Order" was his startling announcement that he would allow the East Timorese to determine their future relationship to Indonesia in a plebiscite. This angered elements in the army, particularly Kopassus, which had played a prominent role in the 1975 invasion of East Timor and also subsequent atrocities. It must surely have angered the Suharto family as well -- they are said to control 40 percent of East Timor's natural resources (including much of its land).

Habibie faces major opposition. Serious investigations -- such as an inquiry into Kopassus involvement in the rapes and murders of ethnic Chinese last year -- have been allowed to lapse quietly. The army was ordered out of the province of Aceh on the basis of clear evidence of its crimes against civilians -- but soon let back in.

Elements in Kopassus, perhaps still answering to Prabowo, continue to use violence. These are not rogue elements, but act with the backing of high-level civilian and military leaders. Indeed, it appears to many that beneath the surface, the "New Order" is still very much in force, supported by the wealth of the Suharto family.

Observers find it difficult to assess the role of Habibie's defense minister, Gen. Wiranto. Repeatedly, Wiranto -- as head of the Indonesian armed forces -- has ordered restraint, but these orders have had little or no impact. This ineffectiveness may derive from a fear that any real reform effort would be resisted, possibly by force, leading to increased violence and upheaval not just in the army but in the country as a whole.

This is why the East Timor crisis must be seen as a symptom of a civilian-military crisis in all Indonesia, and why its resolution will affect the nation's future. Kopassus thugs, identified as key organizers of the terror, have not been particularly bashful about their role. On the contrary, they have displayed severed heads on poles along roadsides, evoking memories of similar displays in 1965, when Suharto seized power, backed by the Special Forces, known later as Kopassus.

Kopassus' actions have stymied Jakarta and Washington as well. Words of restraint from President Clinton and the State Department have gone unheeded. Thursday Clinton was forced to suspend relations with Indonesia's military, though the announcement didn't spell out whether military training or arms sales would also be suspended. Whatever the United States does now, the embarrassing fact is that Prabowo and his thugs enjoyed powerful Pentagon backing, including special training and aid, as recently as last year.

This relationship dates from 1965, when Washington made little secret of its support for the Special Forces, though they played a major role in the killing of more than half a million Indonesians. The Pentagon continued secret aid to Kopassus despite explicit prohibitions by Congress -- in other words, there were secret supporters for Kopassus, and its policy of controlling populations by terror, in Washington as well as Jakarta.

At stake now is whether those in both capitals who seek establishment of an orderly civil society can design a policy to implement that desire. For the United States, this may require honest acknowledgment of past complicity to drive home the point that violence will be condoned no longer.

A high priority would be an embargo on military sales to Indonesia, for the United States is currently the largest supplier of arms to Indonesia.

It may also require recognizing that Indonesia's power structure is fragmenting, and openly limiting aid to those whose style of governing meets international norms. For example, if the United States and the International Monetary Fund withhold aid, they must take steps to ensure that the financial pain is felt by those responsible for the terror and not by the poor who survive on foreign-financed food subsidies.

Above all, it is time to abandon the fiction that East Timor is, or ever was, an integral part of Indonesia. The crisis must be resolved in a way that will strengthen the country's constructive forces.

The alternative, to let violence prevail in East Timor, will almost certainly strengthen the forces of violence elsewhere in the country. Washington faces an unpleasant choice -- but it is, in large part, a choice of its own making.