Nearly six years after its troops and civilian militia laid waste to tiny East Timor, triggering worldwide outrage, Indonesia has begun to repair its military ties with the US.
But the violent 1999 pullout by Indonesia from the now independent half-island state continues to shadow relations between the two former cold war allies. Although President Bush has restored partial ties and pushed for normalization, Congress has refused to restart the training of Indonesian Army officers and the sale of lethal weapons while past abuses go unpunished.
The tussle over how to handle Indonesia's powerful military mirrors a wider debate over the building of alliances in the war on terror, as well as the US security footprint in Southeast Asia. Administration officials argue that Indonesian support in counterterrorism is crucial and that its armed forces are adapting to democratic rule and deserve US support for further reforms.
"We continue to focus on the role the [Indonesian] military have in terms of democracy and respect for human rights. That's not a focus of ours that has gone away," says a US official in Indonesia.
Critics, though, contend that pandering to abusive allies undercuts the push for greater democracy and the rule of law.
"The US has failed to keep its position to protect human rights in Indonesia," says Usman Hamid, coordinator of Kontras, a campaign group in Jakarta that investigates missing persons. "As long as there's no accountability for military officers in human rights cases it's very difficult for us to build the rule of law."
Indonesian troops are accused of extrajudicial killings, beatings, torture, and forced disappearances of civilians in East Timor, Aceh, and Papua.
Hamstrung by congressional limits on military aid, the administration has spent $12 million training Indonesia's police in combating terrorism. Even that program has run into controversy, though. The congressional Government Accountability Office recently claimed that 32 trainees should have been excluded because of their unit's poor human rights record.
Beyond the privileges of combat training and up-to-date hardware, the restoration of full ties with the US would spell a wider rehabilitation for the military, known by the acronym TNI. Officers rankle at their depiction by critics as a pariah force, say analysts and retired generals.
Last year's tsunami in the Indonesian province of Aceh offered a chance to soften that reputation as Indonesian soldiers joined an international aid effort. President Bush and other leaders were quick to praise Indonesian forces for their cooperation in Aceh. Indonesia used the opportunity to press for the sale of spare parts for their ageing cargo planes.
But the divisions of the past were also present: One of the Army officers overseeing relief operations was Maj. Gen. Adam Damiri, who was convicted in 2003 by a human rights tribunal in Jakarta over East Timor violence. General Damiri was later acquitted on appeal, as were all but one of 18 defendants in a widely criticized judicial process that the US called "seriously flawed."
Indonesia and East Timor recently formed a truth-finding joint reconciliation commission to investigate the 1999 events, but it will have no judicial remit.
"The TNI can exert enormous pressure on the government to prevent tribunals looking at its past abuses. That's what we're seeing in the case of East Timor," says Damien Kingsbury, author of "Power Politics and the Indonesian Military."
Indonesian generals have long held a privileged position here. In recent years, though, Indonesia has laid the groundwork for civilian democracy and loosened the TNI's hold on politics. Government officials say US military aid would speed this process by instilling greater professionalism in the ranks and helping to turn Indonesia's 320,000-strong military into a modern force, albeit still focused on domestic threats.
"For the next 15 years, we still need a measured and calibrated role for the army, even in internal security. Civil competence is still weak," says Defense Minister Yuwono Sudarsono.
One obstacle to military reform is Jakarta's shaky finances: A significant chunk of military funds - perhaps as much as two-thirds - come from their own private businesses and pension funds, not government coffers. A recent budget request from the Defense Ministry was slashed in half, says Mr. Yuwono.
Analysts say this self-reliance weakens the hand of civilian reformers who seek to reorganize the TNI's murky finances. Under pressure, the military has begun rationalizing its sprawling assets and opening its books. Yuwono says many companies will be closed and others merged into a holding company by October.