Now the MILF wants to secede and make resource-rich Mindanao a separate Islamic republic.
Murad Ebrahim, said to be in his 60s, is the first MILF leader to visit the palace.
The unit commander pointed to the nearest MILF position just seventy-five metres away.
Emerging from his fortified bunker, the MILF chairman, Salamat Hashim, was all smiles.
About 20 MILF rebels ambushed a truck carrying mostly Christian plantation workers and killed 13 people and wounded 14 others.
Under Estrada, the MNLF's splinter group, the Moro Islamic Liberation Front (MILF), has unleashed a wave of kidnappings and bombings.
The Philippines has signed a framework peace plan with the country's largest Muslim rebel group, the Moro Islamic Liberation Front (MILF).
The progress of the armed forces' campaign against the MILF has forced the militant group to agree a ceasefire and peace talks.
The MILF, created after a split with another rebel group in 1977, had earlier dropped its demand for an independent Muslim state.
Sultan Jamalul Kiram III, now in his 70s and ailing, felt that his request to be consulted on the MILF agreement went unheard.
Having successfully attacked the headquarters of the secessionist Moro Islamic Liberation Front (MILF) two week's earlier, Estrada is looking for new turf to conquer.
In another terrorism trial in the Philippines, a MILF member testified that he had helped JI to bomb a railway station in Manila, the capital.
The separatist war waged for the past 31 years by the MILF and other Muslim rebels on the Philippine island of Mindanao has caused around 120, 000 deaths.
" As for the Muslim secessionists in Mindanao, Estrada's message was succinct: The MILF must accept three demands: "drop secession, drop your criminal activities and drop your arms.
Just as Arafat has to control Hamas, Misuari must coax the MILF and the other militant groups to express their dissent at the polls rather than with pistols.
Mindanao is racked by insurgencies, from the semi-respectable the Moro Islamic Liberation Front (MILF) is engaged in peace talks to the outright criminal, such as Abu Sayyaf in its present form.
It has faced separatist movements in Mindanao, where the MILF is based, and in Jolo, home to the radical Islamist Abu Sayyaf group, which is reputedly linked to al-Qaeda.
In the final stages of the MILF's reconciliation with Manila, four states and four non-governmental organizations, including the Center for Humanitarian Dialogue, supported an advisory panel called the International Contact Group.
One witness said he had trained in the Philippines at a camp of the Moro Islamic Liberation Front (MILF), a local Muslim secessionist group, before bombing a McDonald's restaurant in Indonesia.
The framework deal was signed by the chief negotiators of the government and the rebels, and witnessed by President Benigno Aquino and MILF leader Murad Ebrahim at the presidential palace in Manila.
The MILF announced this week that its leader, Salamat Hashim, had died of a heart attack last month, soon after he had denounced terrorism and promised to eradicate any terrorists from his movement.
Of particular concern are the Moro Islamic Liberation Front (Milf) - engaged for some years in guerrilla warfare against the Philippine army - and the Abu Sayyaf group, well-known for kidnapping foreigners, including several Americans.
The next day we went to the little village of Matanog, still virtually deserted after being caught in the middle of some of the fiercest clashes between MILF fighters and army troops in late January.
Mr Aquino has pledged to do all he can to bring peace to Mindanao - and the MILF knows that if an agreement is not reached now, a future president might not be as sympathetic to their cause.
It also provides for the MILF to "undertake a graduated program for decommissioning of its forces" and says both sides would work for "reduction and control of firearms and the disbandment of private armies and other armed groups".
But the Philippines poses less of a threat to global security now than it did in the 1990s, when al-Qaeda plotted suicide plane attacks here and the MILF invited Jemaah Islamiah, a regional network, to train the bombers who went on to attack Bali in 2002.
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