According to the BBC and Voice of America (VOA) reports, he was riding pillion on a motorbike when he and his driver were ambushed by Pakistani agents, some of whom were wearing burqas.
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.