Countries undergoing democratic transitions experience a wide range of long-term outcomes. Depending on the initial circumstances of the transition, a number of factors can impact on the trajectory of a transitioning country. Factors regarding the organization of the civilian government and the military, which are determined by the history and social context of each country, affect they type of relationship that forms between the military and the government during a democratic transition. This paper focuses on the cases of Indonesia and Egypt as examples of successful and unsuccessful democratic transitions respectively. Egypt and Indonesia had similar initial circumstances at the time of their transitions from authoritarian to democratic modes of government, but each experienced different levels of conflict between the military and civilians. This paper examines how the interaction between factionalism in the military and the government affect the stability of the democratic transition. The presence of factionalism within the military and the elected government may help to reduce conflict throughout reform periods by enabling mutually beneficial political alliances to form between the military and the government.