Cotabato City, Philippines - Weeks before Benigno Aquino III was elected president of the Philippines in 2010, the rebel group Moro Islamic Liberation Front (MILF) hosted a secret meeting with a high-ranking US embassy official and two American dignitaries. The impending national elections and the stalled peace talks in the southern Philippines dominated dinner conversation. Discussing the leading candidate for the presidency, one unimpressed rebel leader said the peace talks were "too complicated for Senator Aquino to understand".

Four years into his presidency, Aquino is set to oversee the signing of a final peace agreement with the MILF, the country's largest Muslim rebel group. Supporters hope the deal creating the autonomous Bangsamoro region will bring an end to 40 years of armed conflict in Mindanao that has killed at least 120,000 people and displaced more than two million. It is expected to be signed this Thursday, March 27.

But now comes the real test: implementing the deal. Threats from armed splinter groups remain, and Aquino still faces doubts over his ability to deliver what he had promised against the backdrop of lingering distrust between Christians and the Muslim minority. Since the 1970s, Philippine leaders - including Aquino's mother Corazon Aquino, president from 1986 to 1992 - have tried and failed to end the violence in the south.

"We all know that this process will be very challenging," Miriam Ferrer, the government's top negotiator, told Al Jazeera. "President Aquino is very committed to use his political capital for the effective implementation of everything that has been signed."

Ferrer said Aquino understands that only a "meaningful autonomy" for the Philippines' estimated 10.3 million Muslims can bring peace in the restive southern islands, and drive economic growth in a region long considered to be the poorest in the country.

A popular president



With an approval rating above 70 percent in December 2013 and presiding over an economy that has grown by an average of 6.3 percent per year during his time in office, Aquino has expendable political capital. He is serving a single six-year term as president, so he does not have to worry about re-election. And his party controls both chambers of congress, which is expected to ratify the agreement.

The fact of the matter is that the Christian community does not want to be part of a Muslim-dominated region. -Steven Rood, Asia Foundation

In exchange for the creation of the Bangsamoro (from the words bansa, or nation; and Moro, or Muslim) and a government with its own budget and police powers, the MILF has given up its violent struggle for an independent state, promising to turn in the weapons of the more than 15,000 rebel fighters.

Steven Rood, Asia Foundation's representative in the Philippines and an adviser to the peace talks, credited MILF Chairman Al-Hajj Murad Ebrahim for being "realistic" during the negotiations, accepting a territory smaller than what was claimed in the 1973 agreement in Tripoli, Libya. That original deal covered areas dominated by Christians, triggering years of bloody conflict.

"While there might be some dreams of sufficient agreement and relations between the communities, the fact of the matter is that the Christian community does not want to be part of a Muslim-dominated region," Rood told Al Jazeera. "They don't mind having a Muslim-dominated region next door, if it is a peaceful one. But even if it is peaceful, they don't want to be part of it."

Still, Aquino pressed on with the agreement, seeing an opportunity to talk to the Muslim rebels following his victory in 2010.

A year after his election, Aquino held a secret meeting with rebel leader Ebrahim, in Tokyo, Japan - an encounter roundly criticised as "ill-advised" by allies of the president, and called "an act of treason" by an unnamed Philippine diplomat.

The high-stakes meeting proved to be the breakthrough in the floundering talks, establishing "trust" between the Philippine government and the rebels, said Kristian Herbolzheimer, of the London-based Conciliation Resources. "That was very important when the two leaders met face-to-face in Japan," he said. "I think that gave very strong signals from the president to his constituency that the government is serious about this, which is why he would meet the chairman of the MILF."

Herbolzheimer, a member of a team of international observers, told Al Jazeera that the agreement is the most significant such deal in the world since the 2006 peace accord between the government of Nepal and Maoist rebels.

'Factionalisation' in Mindanao



But not everyone is in favour of the deal. Julkipli Wadi, dean of Islamic studies at the University of the Philippines, said other Muslim rebel groups such as the Moro National Liberation Front (MNLF) of Nur Misuari have been excluded from the talks.

Despite its peace agreement with the MILF, the Philippines continues to fight armed splinter groups like the Bangsamoro Islamic Freedom Fighters and the Abu Sayyaf [Ted Regencia/Al Jazeera]

He also pointed to the "factionalisation" of different rebel groups in Mindanao. He said that while the MILF negotiated with the government, some of its members who favoured an armed struggle for independence left and formed the Bangsamoro Islamic Freedom Fighters (BIFF), which have been involved in bloody skirmishes with the Philippine military in recent months.

Wadi also said that government negotiators relied heavily on the mediation of Malaysia, which is involved in a separate border dispute with the Philippines on Sabah island. "The two instances of the Sabah siege, the war in Malaysia months ago, and the war in Zamboanga would show that there is something wrong with the peace process," Wadi said.

That three-week standoff in Zamboanga City, which killed almost 200 people and displaced 100,000 civilians, was blamed on the MNLF - the Philippines' original Muslim rebel group, which signed a similar peace agreement with the government in 1996. That deal fell through during its implementation and its leader Misuari has gone into hiding, refusing the overtures of the now more powerful MILF to be part of the new peace agreement.

The Abu Sayyaf Group, which is involved in kidnappings in the south and considered a terrorist group by the Philippine government, is also excluded from the deal.

'The devil is in the details'



The government insists the current peace deal is different, allowing for broader representation from different forces within the region - such as women, youth and indigenous people. The new Bangsamoro government will also receive 75 percent of taxes collected in the region, 75 percent of revenues from metallic minerals and some control of fishing territories.

According to stastics, the region covered by the future Bangsamoro autonomous region, 48.7 percent of the population lives on less than $2 a day [Ted Regencia/Al Jazeera]

Ferrer, the government negotiator, said checks and balances are also in place to ensure accountability and prevent corruption, one of the main problems that eventually led to the breakdown of the 1996 agreement.

"I think a significant difference between the last 10 years and the current period is that a lot of new civil society organisations have been formed to ensure that the governance institutions should not fail in their task," she said.

Amid the "euphoria" of the impending agreement, Rood, a long-time scholar on Mindanao, warned against false expectations of the peace process. "Remember that this is a long process, and we are in it for a long haul," he said. "Nobody underestimates the difficulty of this."

As President Aquino himself acknowledged in a speech promoting the agreement: "The devil is in the details."

Follow Ted Regencia on Twitter: @tedregencia