Philippines bloodbath: was one of last major Jemaah Islamiyah leaders killed?

And if he was, what does it mean?

Philippines forces have suffered one of their biggest single-day losses of life since counterterrorism operations on the southern island of Mindanao ramped up in late 2001.

A police anti-terrorism squad of nearly 400 men, conducting a raid in the village of Mamapasano, where they were looking for two senior bomb-makers connected to the Jemaah Islamiyah (JI) terrorist outfit, blundered into at least two ambushes on Sunday. About 12 hours of fighting ensued, leaving 43 of the Filipino cops dead – as well as, perhaps, Zulkifli bin Hir, a Malaysian national who is believed to be the most senior remaining JI figure who hasn't been killed or captured.  He has an engineering background and is described as a senior bomb-maker.

"There is a high likelihood according to the participants that Marwan was killed in the operations, but this needs confirmation," Philippines Interior Secretary Manuel Roxas told reporters today, using the most popular alias for Zulkifli. "They were able to take pictures, and these pictures will undergo a process to determine whether it was Marwan or not."

Militant roots

JI emerged in Southeast Asia in the late 1990s, with its key members disciples of Abu Bakr Bashir, an Indonesian militant cleric who returned home from Malaysia after the fall of the dictator Suharto in 1998. The group had veterans of the anti-Soviet jihad in Afghanistan and recruited young Malaysians, Indonesians, and Filipinos through a network of affiliated mosques and Islamic boarding schools. The group, which had ties to Al Qaeda, carried out a string of bombings in the Philippines and Indonesia over the course of a decade, most notoriously the twin attacks on nightclubs in Bali in October 2002 that left more than 200 people dead, mostly foreign tourists.

Though its top figures were Indonesians – perhaps most importantly Riduan Isamuddin, or Hambali, who is now detained at Guantánamo Bay following his capture in Thailand in 2003 – the lawless regions of Mindanao and neighboring Basilan and other smaller islands were always important havens for the group. A blend of corrupt officials, gangsterish politicians, and independence-minded Islamist militant groups provided space to train there, and evade capture.

Though the remaining members and sympathizers of JI have largely been pushed into hiding in Malaysia and Indonesia, the Philippines has continued to struggle to assert law and order on Mindanao. It is a heavily armed and wild place, and its problems extend beyond Islamist militants.

In November 2009, 46 people campaigning in Maguindanao, not far from where the bloody firefight took place on Sunday, were gunned down by members of the Ampatuan clan. The group's patriarch, Andal Ampatuan, was a former governor of the province and for decades a confidant of senior politicians in Manila.

Mr. Ampatuan had been term-limited out of office that year – no one had ever dared run against him – and was looking to install his son, Andal Jr., in the top seat. The people slaughtered that November were supporters of Ismael Mangudadato, a rival candidate willing to risk running, waylaid on their way to file papers for his candidacy.

And in February 2013, about 200 armed supporters of the self-proclaimed Sultan of Sulu, a small island chain that runs south and west from Mindanao, sailed to Sabah in Malaysian Borneo with the idea of claiming part of the island as their own. They managed to hold a coastal village for about three weeks before being routed by Malaysian security forces. Some 13 people died.

Mindanao's Muslim community has long resented Manila's control. And though both the Moro National Liberation Front (MNLF) and the Moro Islamic Liberation Front (MILF) have signed peace deals in exchange for autonomy with the government, separatist sentiment remains high.

The MILF peace deal was signed a little less than a year ago, something both Moro leaders (the name for the local population) and Manila hoped would end a 40-year conflict that claimed more than 100,000 lives. But that was never entirely likely. A MILF splinter group, the Bangsamoro Islamic Freedom Fighters (BIFF), rejected the deal, and says it wants to establish Islamic law in the region. The Philippines police say BIFF has been harboring Zulkifli, and it was their militants that police fought with in the first of two engagements on Sunday. 

Peace deal at risk?

The second engagement, if police have it right, is more troubling still. They say the cops withdrew from the initial fight into an area controlled by MILF soldiers, who in turn opened fire. That, obviously, threatens the peace deal.

It's not well-remembered now, but this region of the Philippines was the second place the US military deployed to, after Afghanistan, in the so-called "war on terror" declared by President George W. Bush in 2001. US Marines worked closely with Filipino troops on counterterrorism attacks, based on Mindanao and with a special focus on Basilan, a stronghold for the Abu Sayyaf Group. Abu Sayyaf, like JI, has historic ties to Al Qaeda, and has carried out a string of massacres and kidnaps-for-ransom in the last 20 years.

But the threat was never contained. In 2013, for instance, Abu Sayyaf and BIFF carried out a joint operation involving about 150 men that attacked Army positions on Basilan. And it's not just the MILF that still may fight the government, peace deal or no. Also in September 2013, a splinter group from the MNLF seized and held parts of Zamboanga City for three weeks, trying to declare an independent state. The crisis ended with more than 200 dead. 

Is Zulkifli dead? He's been falsely claimed by Filipino officials to have been killed in the past. But one militant down is nothing compared to the ongoing problems that plague Mindanao, which provide fertile grounds for new Zulkiflis.