The couple were held in Jayapura prison from 1988 to 1990 before the Suharto regime relocated them to Jakarta amidst continual violent protests by West Papuan separatists. The conditions were absolutely harsh, but they had family and West Papua loyalists and die-hard nationalists visited him often. Thom was sent to LP Cipinang prison, while his wife was transferred to Tangerang prison in Jakarta - the capital city of Indonesia. While the conditions in the state penitentiary in Jakarta were comparatively better to that in Jayapura, West Papua, Dr. Thom's healthy gradually deteriorated. Keeping the Wainggai's in Jakarta made it extremely complicated for the Wainggai family to visit them on a regular basis. On March 12, 1996, six years after his transfer to Jakarta, Dr. Thom succumbed to the illness he suffered; he died in jail. Since the Indonesian government did not provide adequate explanation as to the true cause of his Dr. Thom's death, relatives in West Papua believed he died by poison. They believe that Dr. Thom was deliberately positioned - a position that the Council on Foreign Relations echoed in its finding while investigating the issues of West Papua. According to reports, Dr. Thom returned from United States in late 1987 and worked as a lecturer at the Cenderawasih University, West Papua. He was also elevated to a senior position in the "Provincial Planning" office in Jayapura. What triggered his radical move to declare West Papua an independent state remained a debatable issue. It is also debatable why he only planned with a few people prior to the demonstration at the Mandala National Stadium where he was arrested. Some suggested that Dr. Thom may have been unhappy and decided to take his personal anger to the national arena. Jones Sidney of Asia Watch provided a possible explanation for Dr. Thom's decision. According to Sidney, Dr. Thom had a personal goal that was to lead West Papua - formerly Irian Jaya - as governor. In 1987, he garnered enough support to run as a candidate in the 1987 governor's election. Unfortunately, he only received a few votes. Sidney pointed to a popular view that he may have taken his personal dissatisfaction too far. This view suggested that Dr. Thom's decision to declare West Melanesia as an independent state came to being after the election, however, it didn't explain why Indonesian locked Dr. Thom up when he returned from Okayama University, Japan, for six months years back. It seems that Dr. Thom had held this position prior to 1987.