The major militant Islamist network in Indonesia, comprising the Jemaah Islamiyah (JI) and its associated groups, was believed to have been responsible for dozens of violent incidents after 2000, including the Bali bombings of 2002 and 2005. Generally JI sympathized with al-Qaeda’s ideology, openly supported al-Qaeda and other militant ideologues by translating and publishing their work in Indonesia, and sent hundreds of fighters (mujahidin) to Afghanistan for training. The Indonesian militant Islamist groups were not foreign controlled, but they shared some features with a broader militant Islamist network. This essay takes as its point of departure Albert-Laszlo Barabasi’s characterization of al-Qaeda as a matrix of self-organized networks, not a military organization with structured divisions. In Barabasi’s theorization of networks, al-Qaeda appears as a "scale-free network" of a limited number of persons who had accumulated many nodes in a scattered and self-sustaining web. Hence, JI was loosely organized and yet hierarchical, composed of small cells held together by personal loyalties, family, school, and other friendly connections. Faced with intensifying police assaults, militant Islamists increasingly fell back on their networks. Using published reports and the author’s own interviews with relevant individuals, this essay traces the links and nodes of the militant Islamic networks in Indonesia and examines why and how jihadists in Indonesia tenaciously sustained their violent activities.