It's a problem that plagues countries trying to make the transition from authoritarianism to democracy - and one that foreign powers like the US helped create. Indonesia's status as an anti-Communist bulwark during the cold war led to US training and support of the military, particularly Kopassus. Throughout the 1980s and 1990s, the US taught its soldiers intelligence gathering and counterinsurgency skills.
But the US and other Western powers strategically averted their eyes when those lessons were put to sometimes brutal effect at home. Like other parts of the relationship, Indonesia-US military ties have been pared down to almost nothing following the calculated brutality of Indonesia's retreat from East Timor in 1999.
Mugiyanto, who like many Indonesians uses only one name, understands the danger first hand. In March 1998, he was an unknown democracy activist. Then he was picked up by Kopassus, taken blindfolded to an interrogation center, and strapped to a table. Over two days, he was beaten and given electric shocks while being interrogated about his political beliefs and the whereabouts of his friends.
After Suharto's fall, 11 Kopassus operatives were found guilty of kidnapping and torturing Mugiyanto and eight other activists - and then sentenced to 22 months in jail. Their commanding officer, Prabowo Subianto, a son-in-law of Suharto's who admitted he ordered the abductions, was honorably discharged. He's now brokering oil-for-food deals in Iraq on behalf of Minister of Industry and Trade Luhut Pandjaitan - himself a former Kopassus officer. "The forces of democracy still have a hard fight ahead of us,'' says Mugiyanto.
Mugiyanto was one of the lucky ones. Human rights activists say the unit helped kidnap and kill 15 democracy activists in Suharto's final days. Munir believes that 900 more - mostly East Timorese and Acehnese independence activists - disappeared into Kopassus interrogation centers never to be seen again, "But the law makes it very difficult to prosecute unless we can produce a body."