Divisions within the political elite have traditionally played a major role in shaping Indonesia's post-independence civil-military relations. From the ideological conflicts in the 1950s that accompanied the rise of authoritarianism to the cleavages that prevented the formation of a united oppositional front against Suharto in 1998 — disputes between large societal forces have almost invariably benefited the armed forces and their quest for political power. Accordingly, one of the key hypotheses of this study has been that the level of political intervention of the armed forces rises and falls with the intensity of intra-civilian conflict. The previous chapter has pointed to several phases in Indonesia's post-authoritarian transition in which conflicts between civilian groups allowed the armed forces to improve their political standing: the 1999 elections, the constitutional crisis of 2001, and the campaign for the 2004 presidential ballot. However, as the chapter mainly focused on internal military developments, it did not discuss in detail the roots, actors, and social contexts of these intra-civilian conflicts. This chapter therefore analyses the dynamics of civilian politics in the early years of the post-Suharto polity, and explains how the disagreements, disputes, and personal rivalries between civilian leaders impacted negatively on the process of military reform between 1998 and 2004. As in previous chapters, the divisions within the Muslim community serve as a case study to illustrate general patterns of civilian conflict in Indonesia.

In this respect, the chapter concentrates on three main periods in the early political transition that witnessed severe conflicts between Islamic groups. To begin with, the chapter discusses the proliferation of Islamic parties in 1998 and its role in creating the fragmented political landscape of the Habibie interregnum. Demonstrating that old politico-ideological and religious cleavages prefigured the political fault-lines of the early democratic system, the analysis points to the failure of Muslim leaders to unite against the vested interests of residual New Order forces, including the military. Second, the chapter looks at the disputes between crucial Muslim constituencies over the Wahid presidency, arguing that both NU and other large Islamic groups placed their institutional interests above democratic principles. Finally, the discussion turns to the alliances between Islamic figures and retired military officers in the 2004 presidential elections.