Why the Conflict in the Southern Philippines Is Far From Over

The roots of conflict in the Philippines' restive south run deep

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Frederick Alvarez / AFP / Getty Images

Philippine soldiers wear gas masks due to the smell of decaying bodies as they patrol amongst destroyed houses at the site of heavy fighting during the stand-off between government forces and Moro National Liberation Front (MNLF) rebels in Santa Catalina area of Zamboanga City, on southern island of Mindanao on Sept. 26, 2013.

Nine-month-old Sophie will never know her father. Army Scout Ranger 1st Lt. Francis Damian was killed on Tuesday during a firefight in the twisting lanes of Santa Barbara, a swampy neighborhood of nipa-shingled houses and pagadpad trees skirting the mangroves swamps of Zamboanga City in the southern Philippines. Nineteen days have passed since around 200 Moro National Liberation Front (MNLF) rebels marched on the City Hall there and tried to raise the “Bangsamoro Republik” flag to signal independence from the Manila government. Fifteen soldiers and police now are now dead along with at least 126 rebel fighters, while 109,000 civilians have been displaced into squalid camps amid a growing “humanitarian crisis,” according to the U.N.

Rebel numbers have been swelled by reinforcements since the original confrontation on Sept. 9, and although almost 300 MNLF fighters have surrendered or been captured, a significant number remain at large, using Christian hostages as human shields. Zamboanga City is a tropical trading post of around a million people and the principle hub of the national sardine industry. Today, however, gunfire and the stench of rotting corpses characterize the Philippines’ third largest city, situated on the island of Mindanao.

Around 70,000 people are being housed under tarpaulin hastily erected across the bleachers and turf of the city’s main sports stadium. The U.N. Office for the Coordination of Humanitarian Affairs warns of a real risk of disease outbreaks and an urgent need for food, drinking water, health services, cooking utensils and other necessities. Carlos Conde, the Philippines researcher for Human Rights Watch, says the situation is deteriorating quickly with children especially hard-hit. In addition, “we are seeing a rise in gender-based violence because of the length of time people are staying there — rape and molestation are expected to increase,” he says.

(PHOTOSPhilippine Troops Clash with Muslim Rebels in Southern City of Zamboanga)

The southern, largely Muslim provinces of the Philippines have been restive since Spanish colonial times and remain a largely lawless backcountry, where separatist insurgencies have claimed around 150,000 lives over decades of fighting. A recent peace deal with the Moro Islamic Liberation Front (MILF) — which split from the MNLF in 1978 — prompted consternation among other groups, and led to “jockeying for position to be able to influence the situation when it comes to the implementation phrase,” says Richard C. Jacobson, Philippines director for Pacific Strategies and Assessments, a business risk consultancy.

The core MNLF had already signed a peace deal in 1996, but three distinct factions obfuscate the situation. The mainstream Council of 15 is based in Cotabato City and headed by Vice-Mayor Muslimin Sema, dubbed “The Peacemaker,” while the small and shadowy Islamic Command Council is led by Habib Muhahab Hashim. Then there is Nur Misuari’s faction, which is responsible for the current crisis. Misuari is a former university lecturer who founded the original MNLF in 1971, but has been recently marginalized.

The current discord, says Jacobson, is Misuari’s “childish” attempt to “position himself as a powerbroker, but he’s under some sort of self-illusion there because it’s not going to happen.” Jacobson says Misuari “squandered” any hope of playing a prominent political role after his disastrous time as Governor of Autonomous Region of Muslim Mindanao from 1996 to 2002. “But he’s still a player and can still bring some people together and be a troublemaker.”

Local support for Misuari’s MNFL faction is difficult to gauge. Around a quarter of the population of Zambonga City is Muslim, but the recent violence took place in the Islamic quarter of the city, meaning that around half this community has been displaced by Misuari’s followers. (In addition, 10,000 torched homes means that around half the displaced are now also destitute.) This Muslim community is also made up of the members of several tribes, which is why Misuari had to ferry in ethnic Yakan and Tausus supporters from Basilan and Sulu respectively.

(MOREPhilippine Troops Gain Ground Against Separatist Rebels in Zamboanga)

According to Conde, there is little overt support for the MNLF in Zamboanga, but no enthusiasm for the government either — in fact, he expects “simmering resentment against the government to bubble up in the days ahead.” The authorities, therefore, must walk a tightrope. Order must be restored, and yet to crackdown too hard on the rebels might alienate the local Muslim population, rile the other rebel factions, and provide the insurgents with further leverage to use against the central government in negotiations.

“The best way to remedy the conflict is to arrest Misuari and take him through the legal process,” Joseph Franco, associate research fellow at the Singapore-based Center of Excellence for National Security (CENS), tells TIME. Franco points to the 2001 Cabatangan Crisis — orchestrated by Misuari’s late nephew during which dozens of civilians were similarly used as human shields — as evidence that Misuari is a “repeat offender” who believes “he can pull off a crazy stunt and get away with it.” Misuari was eventually captured, having fled to Sabah in Eastern Malaysia, and brought back for trial only for the charges to be dismissed. Such leniency is unlikely to be forthcoming now. “There are lots of rumors of him being charged with treason for what he is doing now but we haven’t seen anything firm from the administration,” says Jacobson.

The conflict is meanwhile being played out around two miles from where the U.S. Joint Special Operations Task Force – Philippines (JSOTF-P) is based. The JSOTF has been instrumental in killing prominent Islamists (such as Zulkifli bin Hir, a senior leader of the Jemaah Islamiyah terrorism network, as well as Abu Sayyaf), and has been behind the apparent deployment of drones. But analysts are split on whether the American military is actively involved in the current standoff, or merely monitoring the situation. The U.S. Embassy in Manila did not reply to TIME’s requests for clarification.

Without doubt, “if the U.S. got involved in some way and it was in the public domain then that would certainly complicate [future negotiations],” says Conde. Emotions are already inflamed. On Sept. 18, Philippine authorities announced that rebellion charges were being prepared against 70 of the 93 suspected members of the MNLF in custody at the time. A dozen of these detainees have since told HRW about alleged mistreatment during interrogation by the police or military — including beating, suffocation with plastic bags, having alcohol poured down noses and other degrading acts. “We are concerned that if the government tries to end this [standoff] then these abuses could continue,” says Conde.

(MOREPhilippines: Hostage Police Chief Persuades 23 Separatist Insurgents to Surrender)

As if circumstances were not thorny enough, the Zamboanga crisis also heralded a separate — now subdued — incursion by Bangsamoro Islamic Freedom Fighters (BIFF) rebels on the nearby island of Basilan, prompting media speculation of coordinated attacks arranged between these disparate groups. However, such an “unholy alliance” between Misuari’s MNFC faction, the BIFF and Abu Sayyuf is based on “flawed analysis,” says Jacobson. “They all started off — even Abu Sayyaf which is supposed to be linked to Al-Qaeda — as criminal gangs that support themselves with extortion and kidnapping, and find it easy to recruit as the region is so underdeveloped.” Any allegiance is based purely on fleetingly aligned goals rather than long-term strategies, he says. Franco agrees, stressing that “clashes there are driven more by parochial concerns such as cattle rustling and land disputes.”

Solving this powder keg situation will be a headache for President Benigno Aquino III, who flew to Zamboanga City on Sept. 13 to “ensure there was no unnecessary loss of lives.” His ten-day visit was the longest time any Philippine President had stayed in Mindanao, indicative of the pariah status the region has long had for the political elite in Manila. But with elections approaching in 2016, he will be desperate to stem the bloodshed — even if that comes too late for  nine-month-old Sophie and the father she will never know.

PHOTOS: The Embattled History of the Filipino South