MANILA, Phillippines — The violence began way back in 1968.
At the time, the Filipino military was secretly training Muslim fighters to occupy an island claimed by Malaysia.
When about two dozen Muslims mutinied, government troops summarily executed them. Word of the killings helped spark a Muslim uprising on the southern islands of Mindanao.
The fighting has since claimed some 150,000 lives.
In March, amid peace talks with Muslim separatists, President Benigno Aquino III traveled to Corregidor Island, the scene of the 1968 massacre.
Aquino's trip sought to instill trust. "It is our responsibility to recognize this event as part of our national narrative," Aquino said in the first official acknowledgement of the massacre. "How can a wound heal if we cannot bring ourselves to even look at it?"
National reconciliation could turn out to be Aquino's legacy.
In October his government signed a preliminary peace agreement with the 12,000-strong Moro Islamic Liberation Front, though many details have yet to be worked out. Known as the MILF, the front has been fighting for a separate Muslim homeland on Mindanao since the mid-1970s.
The agreement calls for the creation of a new autonomous political entity in Mindanao that would be known as the Bangsamoro, and would give Muslims more control over territory and natural resources. The autonomous government would raise its own taxes and direct its own police and judiciary. All of this is supposed to fall into place by the time Aquino's term ends in 2016.
"The breakthrough came when the ever-wary MILF started believing that President Aquino was willing to grant real power to the Bangsamoro and that it should seize the opportunity," said a recent report by the International Crisis Group.
"For the first time, the people in Mindanao are really being consulted" about their future, added Jolly Lais, a community activist in Mindanao who heads the Bangsamoro Solidarity Movement. "Aquino is different. He has become an instrument of peace rather than a spoiler like previous presidents."
Mindanao has always been a land of intractable problems and great potential. It is home to about four million Muslims who consider Mindanao their ancestral homeland dating back to Islamic sultanates established before Spanish Christians arrived in the 1500s. Muslims rose up against the Spaniards and later resisted both the US occupation of the Philippines in the 20th century as well as envoys from the central government in Manila.
These days, the islands make up the breadbasket of the Philippines. They are also home to vast mineral wealth. Yet over the years, Mindanao was largely ignored by the Manila government. As a result, education levels remain low and the poverty rate is much higher than the national average. Adding to the tension was a government resettlement program that sent Christians to Mindanao, turning the Muslim population into a minority.
"For the most part, the central government neglected Mindanao. It was only interested in extracting wealth," said Maria Ortuoste, a Filipino who teaches political science at California State University, East Bay.
But Mindanao's rebel groups have also made a hash of things.
The MILF is a militant offshoot of the Moro National Liberation Front, or MNLF, which formed in 1969 but provoked the split by opening negotiations with the Filipino government in 1970s. In 1996, the MNLF signed a peace treaty that provided limited autonomy for several predominantly Muslim provinces in Mindanao.
But MNLF political leaders were accused of corruption and mismanagement of the autonomous area while, instead of disarming, many fighters became hired guns for local politicians. All along the MILF kept fighting and other Islamic groups, such as the Abu Sayyaf terrorist organization, established beachheads on Mindanao.
Still, the MILF remains the country's largest and best-armed rebel group. Taking it off the battlefield would provide a huge boost for Mindanao by reducing violence and opening the door to more economic development and foreign investment.
The Philippines is already on a role. Last year, the nation posted Asia's second highest growth rate last year. In April, for the first time in history, the Philippines received investment grade status from two of the world's big three credit ratings firms, Standard & Poor's and Fitch Ratings.
"On my last trip to Mindanao, I saw four private jets at the airport with US personnel who were there exploring for natural gas," said Harry Roque, a law professor at the University of the Philippines.
Despite deep suspicions about MILF among non-Muslims, President Aquino and his peace agenda remain popular: Pro-government candidates swept mid-term legislative elections last month. "Peace in the troubled south could well be President Aquino's legacy," noted the International Crisis Group report.
To transform the vaunted framework agreement into a final peace accord, the two sides must hammer out thorny issues such as taxation, wealth-sharing from natural resources, and the integration of MILF fighters into a future Bangsamoro police force. The measures contained in a final peace pact would require approval by the National Congress. And the talks could still collapse, as they did in 2000, 2003, and 2008 amid outbreaks of fighting.
The war has been going on for so long that some still find it hard to contemplate peace. "I've never believed that the peace process will fly," Roque said, "because we have never learned from our history."