This chapter explores the political dynamics of civil–military relations in post-New Order Indonesia. It focusses on the four consecutive civilian leaderships following the fall of Suharto, that is, Presidents B. J. Habibie, Abdurrahman Wahid (Gus Dur), Megawati Sukarnoputri, and Susilo Bambang Yudhoyono, and their interactions with the military establishment. In early years of democratization, the challenges of imposing a civilian control were immense. The military decided to undertake an internal reform with minimum external oversight. Uniformed officers left their position in civilian posts and detached their formal affiliation with Golongan Karya party (Golkar), Suharto’s electoral machine. Nevertheless, this initiative does not include the abolition of territorial commands and military business affairs. This shows the political limitation of civilian presidents in exercising their oversight power. However, we find that such limitation can also be seen as a coping strategy or deliberate no-intervention approach to avoid conflict with the military. MOOTW, in particular, emerged because President Yudhoyono (2004–2014, two periods) saw the missions to be in accordance with his internationalist vision. Meanwhile, the missions, in the eyes of the military establishment, were their Trojan horse to counter-attack any criticism against territorial commands. These two converging interests eventually sustain the ostensibly stable civil–military relations in Indonesia.