Cotabato City, Philippines - On the 20th day of the Islamic holy month of Ramadan, heavy rain flooded the southern Philippine island of Mindanao. This is the heartland of the separatist Moro Islamic Liberation Front's (MILF) armed struggle. As the noon call to prayer echoed through the village of Limbo, the nearby Rio Grande river overflowed, and more than 40,000 people fled their homes. The rebel stronghold of Maguindanao province and nearby Cotabato City declared a state of emergency.

For residents caught in the flood, however, the recent bursts of violence in the region proved to be just as worrisome. At least six people were killed in a powerful bomb blast near a hospital and school in Cotabato on Monday, August 5. At time of this report's publication, no group had yet claimed responsibility for the attack.

A July 26 bombing killed eight people in Cagayan de Oro, a major city 250km north of Cotabato City. Reports blamed the incident on the breakaway rebel group Bangsamoro Islamic Freedom Fighters (BIFF), which later clashed with the military on July 30, leaving eight of its members and a civilian dead. Some fear these incidents could scuttle ongoing negotiations between the government and rebels.

But as the month of Ramadan draws to a close, the main rebel group, MILF, and their followers, said they are praying that the talks, already reportedly at an advanced stage, would result in a final agreement by 2014. That deal could give the area a homeland and a separate government, and would end a conflict that has killed 120,000 people over the past four decades. Negotiations will resume in mid-August in Malaysia after Eid al-Fitr, the celebration of the end of Ramadan.

Von al-Haq, a senior rebel commander overseeing the ceasefire, denied his group's involvement in the attacks. He said MILF would not sabotage a peace process that has a real chance of success.

"Our hands are clean," Haq told Al Jazeera. "We have orders to observe and respect the supremacy of the peace process, and that no-one will intervene or participate in any malicious act against the government."

Haq blamed the latest incidents on the "spoilers of peace".

Ameril Umra Kato, BIFF leader, is a former MILF special unit commander, who was expelled from the group in 2011 for opposing the talks with the government. Kato, who is now in his mid-60s, trained as a cleric in Saudi Arabia.

Dickson Hermoso, an army spokesman, said the BIFF is "hell-bent on derailing" the talks.

Still, there is no turning back on the peace process, Haq said. "We are very optimistic that our peace efforts would bring a solution to the Bangsamoro problem, and hopefully it will be realised soon," he said.

He was referring to the piece of land in Mindanao taken over by Spanish colonisers that was not returned to the mostly Muslim native population when the Philippines gained its independence in 1898. Bangsamoro comes from the words bansa ["nation"] and Moro ["Muslim"]. That unresolved dispute gave birth to the armed Muslim insurgency in the 1970s, during the dictatorship of Ferdinand Marcos.

Inside rebel territory

Inside Camp Darapanan, the main rebel base, residents said they share Haq's confidence.

In a visit to the camp, Al Jazeera met Malhatam Abu and his friends, who were taking advantage of the lull in fighting to watch a basketball game on television at an eatery owned by a fellow rebel. Abu, who became a fighter at 18, lost two of his uncles to the war.

"It was a mess here," said Abu, now aged 47. "I hope there's no more fighting. They need to talk until they reach an agreement."

Outside the shop, 52-year-old Aida Mokadam was keeping an eye on her four-year-old granddaughter, Shainie, while holding her four-month-old grandson, Ajid. She recalled how her family would constantly move to escape the fighting.

Mokadam, whose father was killed in battle, said she supported the talks, so her grandchildren would not have to experience what she went through.



Not far from the rows of huts inside the camp, a bridge connects a muddy road riddled with potholes. Using the bridge's steel pillars as improvised diving platforms, several children from rebel families leapt into the rushing stream below.

Roadmap to peace

There’s a reason for the optimism on the ground, Steven Rood, Philippine representative of the New York-based Asia Foundation told Al Jazeera. Rood is an outgoing member of an international panel involved with the negotiations.



In October 2012, the Philippine government and the rebels signed a peace roadmap, which takes up the political question on land ownership and self-governance – issues that were not fully addressed in previous agreements, leading to more violence.



So far, negotiators have cleared two important hurdles on political transition and wealth-sharing. Soon, they will head back to Kuala Lumpur, to work on a power-sharing framework between the national government and the future sub-state; and on the disarmament of the rebel forces.



In response, the rebel group, headed by MILF Chairman Al Haj Murad Ebrahim, also made major concessions, renouncing its fight for independence, accepting a smaller territory than what was spelled out in the 1976 Tripoli Agreement, and promising to eventually give up the firearms of the estimated 11,000 fighters.



"The MILF very much believes in the sincerity of President Aquino," Rood said. "In terms of his legacy and his personal commitment, they [MILF] are trusting him."



At the same time, the MILF rebels have repeatedly "demonstrated" that it can cooperate with the government in moving the negotiations forward, including "disciplining its own ranks," Rood added.

Philippine President Benigno Aquino III is also betting his political capital and popularity on the deal, despite some doubts in the predominantly Catholic country.

"We are ready to lend the strength of the entire nation to lift up the provinces of Muslim Mindanao, who are among our poorest," Aquino said in his annual address to the nation on July 22. "We will not allow any of our countrymen to be left behind, while others surpass them."

According to the latest government statistics, several provinces in Muslim Mindanao have poverty rates above 40 percent, as of April 2013.

In the end, the voice of talking is more effective than the burst of a gun. Von al-Haq, rebel field commander

But Haq said it was not poverty driving the unrest in Mindanao, but rather the absence of a political solution to their struggle for a homeland.

"If there is a political solution, I can assure you that everything will go with it," Haq said. "Farmers can till their field without fear of bombing, and businessmen can attend to their activities. There's no fear of having untimely loss of lives."

Yet some Christian settlers in Mindanao, who have seen their share of violence, remain sceptical.



At Cotabato's 141-year-old Tamontaka Catholic Church, touted as a symbol of inter-faith unity because of its location within a Muslim neighbourhood, one devotee said he favoured the policy of President Joseph Estrada. During his term, Estrada launched an "all-out war" against the MILF in 2000. He was later ousted, but he remained popular among the Christian community here.

Haq has fought in many wars - including in 2000, 2003 and 2008. "Talking with the enemy is very important and very effective," he said.

"Sometimes, I think the burst of a gun is okay. But in the end, the voice of talking is more effective than the burst of a gun."

Follow Ted Regencia on Twitter: @tedregencia