This thesis has examined the reasons why military reform in Indonesia was only partial and why military influence resurged in the post-Soeharto years. It departed from the theoretical transition literature, combining actor-oriented, structural and cultural perspectives. Empirically the study rests on extensive interviews, newspaper analysis, internet research and analysis of websites, publicly accessible documents, statistics and scientific literature. The study explored for each of the three transitional civilian presidencies between 1998 and 2004 (Habibie, Abdurrahman Wahid and Megawati Soekarnoputri) military responses to civilian reform overtures in areas such as prosecution of human rights violations by the military, the investigation of corruption cases (KKN-Kolusi, Korupsi, Nepotisme) involving the former President Soeharto and his cronies, separatism and Islamic radicalism