This week, the old order and the new squared off in Indonesia. An official inquiry concluded that the violence that erupted in East Timor last year was planned, carried out and abetted by a group that included top-ranking members of the country’s military. The report incriminated 40 members of the armed forces, including Gen. Wiranto, then the military chief and now the government’s coordinating minister for social and political affairs. President Abdurrahman Wahid has demanded Gen. Wiranto’s resignation; the general has demurred, triggering a confrontation between the military and the new government. The outcome is not assured, but Mr. Wahid’s ability to demand compliance with his order will determine Indonesia’s future.

Since taking office last year, Mr. Wahid faced two threats to his political survival. The first was the rebel movements scattered across the vast archipelago that risked to unravel the country. The second was the challenge to his authority posed by the military. The two are linked. Secession challenges reinforced the president’s dependence on the military; the military’s autonomy and its indiscriminate use of force only increased rebel grievances. Any government that claimed to respect human rights was bound to clash with the military.

The report of the Investigative Commission on Human Rights Abuses in East Timor forced the confrontation. On Monday, it released the results of its investigation into the violence in the territory. It concluded that massive human-rights violations had taken place, which “included killings, destruction, slavery, eviction and forced evacuation and other inhuman actions against civilians.” There were “gross violations against the right to life, the right to personal integrity, the right to liberty, the right of movement and to residence and the right to property.” The guilty parties were “people who are operating in the field at that time, including the militias, military and police. . . mass killings claimed the lives mostly of civilians. They were conducted in a systematic and cruel way. Many were committed at churches and police headquarters.”

The panel called for the establishment of a special court to try cases alleging violation of human rights and crimes against humanity. It also recommended the prosecution of dozens of people, among them Gen. Wiranto and five other generals. The generals were accused of not providing the security they had promised. Mr. Wahid had said that he would ask for Gen. Wiranto’s resignation if he was incriminated; the president wasted no time in acting when the panel did just that.

The general refused to submit his resignation, preferring instead to accuse the panel of having political motives, a move that only increased the stakes. Mr. Wahid has removed the fig leaf of a “resignation” by demanding that he quit. The general clings doggedly to his post, prompting fears of a military backlash — including a coup — against the government.

This is only the most recent, and most dangerous, example of the military’s refusal to quit playing kingmaker in Indonesian politics. Under former President Suharto, the armed forces adopted the “dwifungsi” doctrine, which gave them a role as protectors of the government from external and internal threats; that was a blank check to meddle in politics. President Suharto could keep them in check; now the world will see whether Mr. Wahid can as well.

The military has challenged the new order since its birth. Last September, the armed forces tried to ram through legislation that would have given them new powers in the event of an emergency. Public uproar forced a retreat. A few weeks ago, a military spokesman who had persistently criticized the government challenged the president’s right to fire him. He, too, was dismissed. Gen. Wiranto poses a threat of a different kind. He has pretensions to the presidency, and the allies to make them real. Concern has prompted the United States and other friends of Indonesia to warn against a coup attempt.

It is tempting to view the political situation in Indonesia through a prism that frames it as a confrontation between the past and the future. That is an important dimension — especially since stability is a prerequisite to the return of much-needed foreign investment — but it is only part of the picture.

The looming confrontation in Jakarta also represents a clash between forces demanding justice for the crimes committed against innocent people and the perpetrators who put themselves about the rule of law. The showdown is between Mr. Wahid, president and embodiment of the democratic aspirations of the Indonesian people, and a military that puts its own interests above all others. President Wahid and his allies, the people of Indonesia, deserve our support in the fight.

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