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The quest for justice in East Timor gathered momentum last week with the submission of reports from two separate investigations into the rampage that occurred last September after the province voted for independence. But the stir raises profound questions of how to deal with transitional justice, pitting principles of democracy and sovereignty against universal values of human rights.

Which path to justice is chosen is crucial. It must do two things simultaneously: squarely address the atrocities committed against the people of East Timor last autumn and at the same time encourage Indonesia’s own search for accountability, which has the potential for effectively reinventing its entire political culture and forming a basis for a true democracy.

Since this decision will also set a precedent for further reconciliation in the embattled region, it must be made with full awareness of the unintended consequences it may bring about. The best option is one that will encourage democracy in both countries by allowing each of them fair representation in the process.

When the Indonesian government inquiry released its report, the comprehensive and conclusive findings stunned the international community. After four months investigative work on the ground, the commission, known by it’s Indonesian acronym KPP-HAM, held 200 people — including then military chief Gen. Wiranto and five other generals — “morally responsible” for aiding a campaign of rape, murder and torture in the wake of the August vote that led to independence for the half-island former Portuguese colony.

The announcement of the domestic inquiry’s results came just days after U.N. investigators submitted their own report to U.N. Secretary General Kofi Annan. Since then, the two commissions’ recommendations have spurred a tug-of-war debate between those who believe East Timor should have an internationally appointed panel of judges try the case (similar to the Nuremberg or former Yugoslav war-crimes tribunals) and those who believe Indonesia should seek to prosecute military officers within Indonesia’s own court system (as Cambodians initially envisaged doing with respect to the Khmer Rouge).

However, the chance of achieving adequate justice through either of these proposals is slim.

To be sure, any trial and conviction under the Indonesian legal system would be ground-breaking in itself, given the limited rule of law in that country and the comparative infancy of its democracy (the first fully democratic elections were held in June 1999).

Yet, although Indonesian President Abdurrahman Wahid has said Wiranto should be prosecuted and resign from his post as security minister, he has also promised to pardon the general if he is convicted. In addition, a draft law that attempts to redefine the basis under which Indonesians can be tried for human-rights violations is up for consideration in the Parliament in Jakarta at the end of the month. If this law — which includes a specific clause allowing for retroactive prosecution — does not pass, the cycle of impunity will be continued. A cushy retirement for a top general only in his early 50s is hardly adequate retribution for the terror unleashed on hundreds of thousands of Timorese during last year’s rampage.

A U.N.-sponsored war-crimes tribunal would arguably raise the profile of the East Timor case and set an example and possible deterrent for future atrocities. But it is unlikely that Security Council members Russia and China would refrain from vetoing an international tribunal. It would make no sense for either country to support such a mechanism when both could at some point be singled out for their own domestic ethnic repressions.

A third solution has recently been proposed by U.N. legal specialists in East Timor working for the U.N. Transitional Authority in East Timor. This option proposes that trials should be carried out in the East Timorese capital of Dili by a mixed team of foreign and Timorese jurists. But it excludes Indonesia as a participant in the process.

Indonesia does not have jurisdiction over the military-sponsored Timorese militias who have been indicted by both KPP-HAM. Nor does East Timor have power to prosecute the Indonesian army brass. Because the crimes were committed on the half-island formerly under Indonesian control and many of the indicted Timorese have escaped to other parts of Indonesia, it would be fitting for the two countries to cooperate.

The world must encourage Indonesia to reconcile with the East Timorese, while giving it the space to create its own process of transitional justice, allowing for a balance between accountability and political stability.

This can be done through the establishment of either a single international tribunal, including both Indonesia and East Timor, or separate but parallel and cooperative processes, possibly under the guidance of the international community. But to be effective, its central aim should be to cautiously yet comprehensively address the past, present and future role of the Indonesian military.

Since Indonesia achieved independence from the Dutch in 1945, the army has always played a dominant role in the nation’s politics. The crucial role of maintaining stability across the 13,000-island archipelago has led the government to repeatedly ignore the tactics used to ensure that stability. As a result, top generals have traditionally been appointed to gubernatorial posts in Indonesia’s key provinces, and the military has held a portion of the appointed seats in Parliament.

Wiranto represents the army-hardliner link to the previous Suharto regime. His role is so great that some even conjecture that reform-minded Wahid planned to use the human-rights inquiry as a wedge to resolve his own power struggle with the military.

The issue of accountability has indeed put the power struggle into focus in Indonesia — and the winner will be the one who has effective control over the military. Yet the vehicle through which accountability will be sought will bring about a new dynamic, and the decision will have its own consequences. It has the potential to redefine Indonesian civil-military relations and will have direct ramifications for ongoing irredentist movements in Aceh, West Papua and the Moluccas, which will, in turn, affect stability in the Southeast Asian region as a whole.

Seeking adequate justice for East Timor is imperative. But should it come at the cost of still greater instability in the region?

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