Al-Qaeda may be the biggest, baddest terrorist supergroup on the planet, but it is by no means the only such menace. In Asia, as security and counterterrorist forces came online after Sept. 11, it became apparent that regional networks, often acting in concert with al-Qaeda, posed the greatest local threats. Of these, Jemaah Islamiah (JI), remains both the profoundest enigma and greatest worry. The outlines of the organization are frightening enough: possibly hundreds of operatives, cells throughout the region, and responsibility for a string of hijackings, bombings and bank robberies stretching back to 1994. Hambali, the brains behind the group, remains at large. And a recent wave of arrests in the Philippines makes clear the organization may be regrouping—and still has ties to nations throughout Asia.

In the lobby of the well-appointed East Asia Royale Hotel in the Philippine port of General Santos City, the three Indonesian businessmen and their Thai colleague made an unremarkable group. Foreigners who come to this scruffy entrepot in southern Mindanao are usually a bit fishy: this is the center of the country's tuna industry. And sure enough, on the morning of March 12, the four men checked in under the name of a firm called Century Tuna.

But these foreigners were here trawling for a different kind of catch, the type that swiftly attracted the attention of the Philippine police. By the following evening, the Indonesians—Agus Dwikarna, Tamsil Linrung and Abdul Jamal Balfas—were under arrest in Manila on charges of possession of bombmaking material. A search of their luggage yielded detonating cord, blasting caps and a small quantity of C4 military explosive. The men deny the charges and say these items were planted in their bags.

Philippine authorities report the men are connected to JI. In the past two years alone, JI has been implicated in Philippine and Indonesian bombings, and last December, Singaporean police foiled the group's plans to bomb local American targets. Police now worry JI is recruiting and training Islamic extremists from throughout Southeast Asia and forging ties with other radical groups to export its brand of holy war across the region. Says a Southeast Asian security official: "The feeling in the region is that the arrests in Singapore, Malaysia and the Philippines are all pointing to a group based in Indonesia." The Indonesian government's indifferent waging of the war on terror has frustrated its neighbors and allowed the country to remain JI's best bastion in the region. This latest wave of arrests indicates that JI's web of connections may extend even to the highest levels of Indonesia's political establishment.

Police say the three Indonesians and their Thai friend drove inland from General Santos City toward Marbel where they met contacts from the Moro Islamic Liberation Front (MILF), Manila's main southern guerrilla foe. The foreigners were taken to insurgent-controlled areas to meet local MILF leaders and possibly other Indonesians operating underground with the MILF.

The Thai man, Prasan Sirinond, has disappeared, and police suspect he too has JI connections, raising the possibility of a terrorist cell in Bangkok. But for the moment, investigations are centered on the Indonesians, particularly Agus and Tamsil. Both are from South Sulawesi, a province that has had a tradition of militant Islamic separatism dating back to the '50s. Tamsil has mainstream political connections: he was until recently treasurer of the National Mandate Party, whose leader Amien Rais is speaker of the People's Consultative Assembly, Indonesia's highest legislative body. The leader of the Java-based Laskar Jundullah paramilitary group, which has been implicated in a bomb attack on a Kentucky Fried Chicken outlet in Makassar last year, confirms that Agus Dwikarna is its South Sulawesi commander.

It was in the memory of Agus' cell phone that Philippine police claim to have found the home number in East Java of Fathur Rohman al-Ghozi, the 31-year-old JI operative arrested in Manila this January and charged with the Dec. 30, 2000, bombings in the Philippine capital that left 22 dead and some 100 injured. By his own admission, al-Ghozi had used General Santos City as a base to store explosives for actions outside the Philippines. Police believe the three Indonesians had visited the city to investigate the damage to JI operations due to al-Ghozi's arrest and to reaffirm the group's connections with the MILF.

Security officials suspect other JI cells remain active in the Philippines, possibly working with the MILF. Meanwhile, throughout Southeast Asia, the workings and whereabouts of Jemaah Islamiah remain as mysterious as they are frightening.

With reporting by Zamira Leobis/Solo, Nelly Sindayen/Zamboanga and Jason Tedjasukmana/Jakarta