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On 12 June 2002, the Special Panel for Serious Crimes of the Dili District Court, East Timor, issued an indictment against Paulo Gonsalves, Marcelino Leto Bili Purificasao and Rosalino Pires, respectively the commander, deputy commander, and a member of the Halilintar Merah Putih militia group based in the subdistrict of Atabae in East Timor. According to the allegations, several victims alleged to be supporters of East Timor’s independence from Indonesia were detained, beaten, and raped by the three members of Halilintar Merah Putih in the period between February and September 1999. In that period, numerous pro-Indonesian militia groups operated throughout East Timor attacking pro-independence supporters with the goal to gain autonomy within Indonesia.

Following the decision of the Indonesian government taken in early 1999 to offer East Timor the opportunity to vote for independence or for autonomy within the Republic of Indonesia, violence erupted in East Timor. The defendants in this case took part in a widespread or systematic attack directed against civilians that were in favour of an independent East Timor. One of the accused, Herman Sedyono, was the Bupati (District Administrator) of the Covalima District, one of the 13 districts in East Timor. As such, he was bearing the primary responsibility for maintaining peace and security in the region. Most of the other accused were Commander or just member of the Indonesian security authorities (TNI) or the Indonesian police force (POLRI), which were both promoting autonomy within the Republic of Indonesia.

In 1999, the Mahidi and the Laksaur pro-Indonesian militia groups, with the help of the TNI and POLRI, and with support from the Covalima District administration, repeatedly committed attacks against the Covalima population (mainly against those that were in favour of independence). The attacks involved crimes such as unlawful arrests, destruction of property, detention, and murder. The 16 accused were charged with encouraging, assisting and failing to stop, arrest or prosecute the perpetrators of the crimes.

In 1990, several Mexican nationals, executing an assignment from the United States Drug Enforcement Agency, abducted one of the persons suspected of involvement in the murder of a DEA official. He was eventually acquitted of all charges by an American Court and returned to Mexico.

Alvarez-Machain attempted to take legal action against the Mexican nationals (including Jose Francisco Sosa) involved in his arrest, and against the United States. In first instance, the Court rejected the action against the United States, but established Sosa’s liability. The Court of Appeal confirmed Sosa’s liability, establishing that his involvement in the arbitrary arrest and detention of Alvarez-Machain constituted a breach of the ‘law of nations’. In the current en banc hearing and opinion the Court of Appeal affirmed its earlier conclusion concerning Sosa, and also established liability of the United States: Machain's arrest, planned by the DEA in the United States, was found unlawful.

On 1 December 2003, Trial Chamber II of the ICTR delivered its judgment on the case against Juvénal Kajelijeli, former bourgmestre (mayor) of Mukingo. In its verdict on the 11-count indictment, the Tribunal found him guilty on three counts: genocide (count 2); direct and public incitement to commit genocide (count 4); and, extermination as a crime against humanity (count 6).

He was sentenced for genocide and extermination as a crime against humanity with imprisonment for the remainder of his life, and with 15 years imprisonment for direct and public incitement to commit genocide. The sentences would be served concurrently. He was given credit of five years, five months and 25 days for time already spent in custody.

The Accused was acquitted of the following three counts: conspiracy to commit genocide (count 1); rape as a crime against humanity (count 7); and other inhumane acts of crimes against humanity (count 9). Earlier, on 13 September 2002, following a Defence motion, the Tribunal found that the Accused was not guilty of the two counts of war crimes—i.e. the charge of violence to life, health and physical or mental well-being of persons (count 10); and causing outrages upon personal dignity (count 11).