A Muslim woman releases a dove as a symbol of peace during a rally against the Islamic State in Jakarta, Indonesia, in 2014. The banner reads: "ISIS is not Islam's voice. Stop killing journalists.” (Tatan Syuflana/Associated Press)

The Islamic State hasn’t had much success in recruiting militants among the vast Muslim populations in Southeast Asia. But what happens when the caliphate’s capitals in Syria and Iraq are destroyed, and hundreds of foreign fighters from Indonesia, Malaysia and the Philippines try to go home?

Experts here in Australia see the counterterrorism challenge as a regional problem, rather than simply an affliction of the Middle East and North Africa. They fear that a potentially dangerous new phase may lie ahead, as the jihadists look for new sanctuaries.

Governments in Southeast Asia have been working quietly with the United States, some for more than a decade, to monitor and try to disrupt radical Islamist groups, and they’ve had considerable success. The United States helped train an Indonesian police unit known as Detachment 88, which has largely destroyed Jemaah Islamiah, the al-Qaeda affiliate responsible for the 2002 Bali bombing that killed more than 200 people.

But the prisons, slums and youth gangs of Southeast Asia provide an ecosystem where terrorism could fester anew, experts say. Islamic State operatives in Syria have tried to reach out to these potential jihadists, as in the bombing in January in Jakarta that killed eight people, for which the Islamic State claimed credit.

Most Southeast Asian Muslims reject such violence, but to plot mass-casualty attacks, it takes only a tiny fringe. “We have more activity among jihadi groups than at any time in the last 10 years,” said Sidney Jones, director of the Jakarta-based Institute for Policy Analysis of Conflict, in a speech in April in Australia.

The would-be catalysts for violence are the jihadists who traveled from Southeast Asia to Syria and Iraq. Experts estimate that this foreign-fighter network includes as many as 500 to 600 Indonesians, 110 Australians, about 100 Malaysians and a small number of Filipinos. This Southeast Asian contingent is far larger than the number who traveled to Afghanistan to join al-Qaeda before Sept. 11, 2001. And in Iraq and Syria, the volunteers have fought and killed.

“We haven’t yet seen the worst” in Southeast Asia, said Aaron Connelly, a research fellow at the Lowy Institute, a foreign policy think tank in Sydney that arranged my visit to Australia.

Experts worry about three risk factors that could expand the currently small terrorist network in Southeast Asia: declaration of an Islamic State affiliate in the lawless jungles of the southern Philippines, recruitment of new Islamic State volunteers in the Malaysian army and a jihadist push by released prisoners in Indonesia.

Islamic State fighters from Southeast Asia proposed a Philippines caliphate in a video that was released in June. This region could be a haven for jihadists; a Muslim revolt against the Catholic-dominated government has been simmering there for a century.

“Kill the disbelievers where you find them and do not have mercy on them,” Abu Abdul Rahman al-Filipini urged in the video, which was recorded in Raqqa and translated by SITE Intelligence Group .

In Malaysia, the army has been a worrying source of recruits. The country’s defense minister told parliament last year that at least 70 former members of the military volunteered for the Islamic State. Malaysian authorities long wary of Western help have been working closely with the United States and Australia since last year to contain such jihadist activities.

In Indonesia, police have campaigned aggressively against jihadists, killing or imprisoning many leaders. But as in Iraq and Syria, the prisons have been a breeding ground for extremism. Based on her research in Jakarta, Jones argued in a recent study: “The prison system — where plots are hatched, travel arranged and [Islamic State] supporters recruited — needs urgent attention.” Experts worry that as many as 200 former jihadists are due to be released from Indonesian prisons soon.

For nearly 15 years, the United States has been quietly funding counterterrorism efforts in Southeast Asia. A study published last year by the Combating Terrorism Center at West Point noted that the United States had provided $441 million in security assistance to the Philippines, mostly for its military, and $262 million to Indonesia, mostly for its police. Police efforts appear to be a better bet: Terrorist attacks increased in the Philippines by 13-fold between 2002 and 2013; attacks declined 26 percent over that period in Indonesia.

The Islamic State may lose its caliphate in Syria and Iraq. But there could be a boomerang effect — a bigger jihadist threat in countries to which the fleeing fighters return.

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