The government has denied the accusation and has insisted it has fulfilled its obligations under the agreement, which was signed by President Fidel V. Ramos for the state and by Nur Misuari for the MNLF.

MNLF and influential Muslim leaders said lapses in the implementation of the historic treaty could damage the future of Mindanao in many ways:

First, they give Moro Islamic Liberation Front (MILF) leaders doubts about government sincerity in giving Moros meaningful autonomy and can upset the continuing peace talks between government and MILF negotiators in Kuala Lumpur. If the GRP-MNLF Peace Agreement is a failure, what incentive does the MILF have to remain at the table?

Second, the lapses could fan greater MNLF resentment against Manila and summon retired and active guerrillas to resume their rebellion against the government. An MNLF-MILF alliance would be lethal to the government and the military, analysts said.

Third, they threaten the stability of the ARMM (Autonomous Region in Muslim Mindanao) government and could cause its dissolution. The Autonomy Act that created ARMM, although criticized by the MNLF as violative of the spirit of the peace agreement, still offers a reasonable option to the Muslim demand for total independence.

Fourth, a breakdown in peace and stability could cause major donor Countries -the United States, Japan, China, the European Union to reconsider their official development assistance to Mindanao and withdraw their support from the region altogether.

Fifth, a deterioration of conditions imperils the Philippines’ standing with the Organization of the Islamic Conference (OIC) and could isolate Manila from the Muslim world.

The 1996 Final Peace Agreement brought a two-decade rebellion by the MNLF against Manila to an end and restored peace to Mindanao and outlying islands.

A demand by the Muslim rebels for total sovereignty, occasioned by government neglect, Christian bias, Moro-bashing, disrespect for Muslim culture, religion and traditions, ignited the Misuari-led rebellion.

Looming in the background was the centuries-old strife between the Muslims and a succession of colonizers, including Spain and the United States, helped along by Christian mercenaries, opportunists and landgrabbers.

Some historians say the massacre by a secret Armed Forces command of at least 28 among a group of more than 200 Moro  military trainees in Corregidor in 1968 hastened the launching of the MNLF as a secessionist movement.  The 28 had mutinied because of the poor food and unhealthy condition in the camp and the mission of the so-called Jabidah Operation they were being trained for.  Chosen for being bahasa Melayu speakers, their mission was to serve as a fifth column in the invasion of Sabah.

The war cost thousands of lives among the Philippine military, the MNLF and civilians, maimed and wounded thousands more, destroyed billions of pesos in property, set back the education of Muslim youths and worsened economic and social conditions in Mindanao.

The end gave the AFP rest, saved the government billions in resources, launched a period of reconstruction, and what could have been a new era of trust between Manila and Muslim Mindanao.

The 1996 agreement gave the Autonomous Region of Muslim Mindanao a self-rule concept provided for in the 1987 Constitution.

It prompted the surrender of Nur Misuari and his transformation from guerrilla to government leader with his election in 1996 as ARMM governor.

Hundreds of MNLF guerrillas received amnesty and were integrated either into the AFP or into the Philippine National Police. The MNLF gained observer status in the OIC.

Full economic aid never came, according to MNLF and civilian leaders.

Misuari’s leadership, however, was short-lived. The government charged him with mismanagement, corruption and incompetence. He had actually improved on the way the ARMM was managed by earlier governors.  And, like his two predecessors, he suffered from the ARMM’s not being funded properly.

In 2001, he was accused of leading a brushfire rebellion against the state. He fled to Malaysia, where the police hunted him down, arrested him and deported him to Manila. He has been in detention since, although he has not been formally charged. His trial has not begun.