On September 21, 1999, Thoenes was killed by soldiers from a company of the Indonesian Army's
Battalion 745 as the unit withdrew from the territory, carrying out a deliberate, government-directed, scorched-earth policy as it went. These murders were just one in a string of similar incidents that marked the passage of the unit westward along the coast-road toward the Indonesian border. Thoenes was riding
pillion on a local motorcycle taxi in the neighborhood of
Becora, just east of
Dili, when he encountered the column of motor-cyclists and heavy lorries as it approached Dili from the opposite direction. Australian-led
UN peace-keepers discovered Thoenes’ body with gunshot-wounds in the back-yard of a house on a side-road. It was concluded Thoenes had been moved off the road to delay his being found and that he had also been shot at close range, with deliberation. Florindo Araujo, Thoenes' motorcycle taxi driver, told reporters that he was stopped by at least six men wearing gray Indonesian police uniforms at a roadblock while en route to Becora. Araujo and Thoenes sought to flee. Araujo managed to reach cover in the bush nearby and hide. He witnessed the execution of the injured Thoenes at the road-side. Two Indonesian army officers, Lt. Camilo dos Santos and Maj. Jacob Djoko Sarosa, were later blamed for his murder by a UN special investigator. Thoenes' death marked the first time a foreign reporter was killed in East Timor since 1975. In 2000, he received a posthumous
press freedom award from the
Washington D.C.–based
National Press Club (NPC). The incident was the subject of a documentary, broadcast in October 2013, by fellow Dutch journalist
Step Vaessen. On September 21, 1999, Vaessen was reporting from central Dili, together with her husband Andries, for
Nederlandse Omroep Stichting. She still works in the region, now as the
Jakarta correspondent for international broadcaster
Al Jazeera English. The film was part of the
Al Jazeera Correspondent series and featured an interview by the veteran South-East Asia journalist
Jon Swain, who narrowly avoided the same fate later that day, nearby on the same road. Vaessen interviewed General
Wiranto, the overall Indonesian military commander at the time and former Presidential candidate, and
BJ Habibie the President of Indonesia in 1999. The General suggested that the military had to obey government policy, whilst the President suggested he had no personal responsibility for the military's actions. The international community tends to indict only those who are already disowned. ==Legacy==