Terry Mccarthy, Jakarta – Sitting in an office deep inside the Istiqlal Mosque complex in the center of Jakarta, Komaruddin Rachmat looks like a man of peace. Yet two weeks ago the soft-spoken activist armed 30,000 rough-hewn Muslim vigilantes to intimidate students protesting for democracy. As the muezzin's call to prayer echoes down the marble corridors of Southeast Asia's largest mosque, Komaruddin dispassionately contends that Muslims had to turn out to support the presidency of B.J. Habibie – seen as sympathetic to Islam – and that the students were being controlled by Catholics and Marxists.

Behind Komaruddin's gentle manner lies a deep-seated confidence that his time has come – and a determination to take whatever measures necessary to make Indonesia a more thoroughly Muslim country. Komaruddin is chairman of FURKON, an umbrella organization of 24 Muslim groups. He says he visited Habibie in early November and told the President these groups would "protect" the coming parliament session from the expected student protests. Living up to his word, he bused "volunteers" (many said they were paid about $2.50 a day) into Jakarta the week of the meeting. The vigilantes – known in Indonesian as Pam Swakarsa, or security volunteers – were given bamboo sticks and white headbands inscribed with Arabic characters and sent around the city in open-bed trucks to taunt the students. Twelve people died in clashes on the last day of the session. They include four of Komaruddin's men, beaten to death by residents of Jakarta's Cawang and Bendungan neighborhoods who resented the vigilantes' heavy-handed tactics. The deaths don't seem to faze Komaruddin much. "This is a good opportunity for Muslims in Indonesia now," he says. "We don't want to lose this chance."

As Indonesia staggers in search of a new political model after 32 years of Suharto's dictatorship, Muslim groups sense a political opportunity. And that is starting to worry many secular Indonesians. With elections tentatively set for next June, some fear the intervening period will see more outbreaks of violence as political groups become polarized and resort to intimidation rather than dialogue. The battle lines are being drawn. "This is not a moral movement," says Ahmad Sumargono, vice chairman of the Indonesian Committee for World Muslim Solidarity, referring to Habibie's opponents. "It is a political power struggle. Non-Muslims are afraid they will be marginalized by an election." Counters Frans Seda, a Catholic economist who served as a finance minister under both Sukarno and Suharto. "We have been trapped into this. To be against Habibie now is to be against Muslims."

Islam in Indonesia is, on the whole, far milder than extremist strains seen in the Arab world. But Habibie's rise has given political voice to some purists; the President and his ministers, lacking any other popular base, seem eager to court them. The traditionally secular military, now confronted with strong demands for rapid democratization, is also working with the resurgent Islamic groups. "The military and the Muslims are forming an alliance," says Endy Bayuni, managing editor of the Jakarta Post. That, many fear, is a lethal cocktail. "They are playing with fire," says former environment minister Sarwono Kusumaatmadja. "I think we're at risk of a very violent mass-based conflict."

The use of religious groups and symbols for political aims does not end with the vigilantes. Small, unidentified bands of Muslim protesters have targeted newspapers and TV stations, complaining that coverage of anti-government demonstrations has been overly sympathetic to the students. "This is the beginning of the destruction of religion, because it's being used for political purposes," says Ali Sadikin, a former Jakarta governor. Sadikin himself is under investigation, along with 19 other prominent opponents of Habibie, for allegedly masterminding an attempt to topple the government. Sadikin dismisses the charges as a ploy to shift attention from the military's shooting of unarmed students two weeks ago.

Amid all the rumors and disinformation swirling around Jakarta last week about who was manipulating whom during the protests, one thing had become clear: the Muslim-secular struggle will be a defining feature of post-Suharto Indonesia. Komaruddin has a clear idea of how he would like to create a Muslim nation, a process he says will take about two generations. "We know the Muslims in Indonesia are very lax, and they have been quiet for so long," he says. "But now is the time for Muslims to advance, in politics and economics too." The residents of many Jakarta neighborhoods saw Muslims advancing two weeks ago – with bamboo spears and angry slogans – and they did not like what they saw.