The peace between the Philippine government and the MNLF (established by the 1996 FPA) is at best an imperfect peace. While large-scale hostilities have stopped, frustrations and complaints have been repeatedly raised by the mujahideen.
At the local level, some MNLF mass-based communities became ‘peace and development communities’ benefiting from livelihood, cooperatives, and other projects with funds coming from international and foreign development organizations. Yet according to Santos (2010a), the MNLF felt that the peace process, particularly Phase 1, was being concluded unilaterally, and that its important socio-economic development elements were not being satisfactorily implemented. The introduction of Phase 2 was signalled by the 2001 New Organic Act for the ARMM (Republic Act No. 9054) which the MNLF saw as violating aspects of the 1996 peace agreement, notably control over strategic minerals. It viewed the expanded ARMM (to include Basilan province and Marawi City) as too weak to address even basic health and education needs in some ARMM provinces (which are admittedly among the poorest in the country.
Frustrations with the perceived failure to implement the peace agreement and Misuari’s feeling that he was being eased out of his positions of authority in the ARMM and MNLF sparked an outbreak of hostilities between the government and Misuari’s forces in Sulu and Zamboanga in November 2001. These developments led to Misuari’s arrest. The MNLF leader started to view the peace agreement as a shackle from which the MNLF would be better off freed to pursue a new phase of struggle for independence.
To be sure, warlord clans such as the Ampatuans beholden to the central government in Manila took over control of the ARMM largely through the active support of Malakanyang during Arroyo’s tenure. The MNLF had its own share of mistakes, including a failure to maintain or recreate itself either as a politico-military mass organization or as a political party. Concessions, co-optation, divide-and-rule, demobilization, splits, and worse, political defeat or marginalization through its own mismanagement of the ARMM (and its funds) have degraded the organization to a moribund status.
Thus it could be said that the MNLF lost both the war and the peace. Since then, splits have further weakened the movement. The MNLF (Misuari faction) showed signs of revitalization through armed hostilities with government in February and November 2005. This residual hostility was the result of the failure to integrate a number of armed fighters (and their relatives) into the Republic’s security forces. To the extent that the MNLF has not returned to the battlefield and has not conducted conventional warfare as before, one can argue that the 1996 peace agreement was successful. To the extent that legitimate grievances are not fully addressed, then the peace is imperfect.
The weakness of a still armed MNLF has helped spawned more aggressive anti-state rivals (Moro Islamic Liberation Front [MILF] and the Abu Sayyaf) as well as allowed conservative and reactionary elements like the Ampatuans (is the incumbent ARMM governor Mujiv Hataman, who is reportedly involved in the murder of a congressman from Basilan province, any better?) to take control of regional autonomy structures. To that extent, peace remained elusive in Muslim Mindanao. As a result, the Philippine government is currently engaged in a multi-pronged effort to maintain peace and order combat the Abu Sayyaf and other criminals, and at the same time to forge peace with the MILF and perfect the peace with the MNLF. On the agenda of the GPH-MNLF talks to implement the 1996 FPA are the key issues including amendments to the organic law of the Muslim autonomous region (RA 9054), the Bangsamoro development assistance fund (BDAF), and suitable formulas for revenue sharing. These are among the challenges confronting the Noynoy Aquino government.
Abat, Fortunato. 1993. The Day We Nearly Lost Mindanao: The CENCOM Story. San Juan Manila: Fortunato U. Abat FCA, Inc.
Abinales, Patricio. 2010. Orthodoxy and History in the Muslim-Mindanao Narrative. Quezon City: Ateneo de Manila University Press.
Ahmad, Aijaz. 1981. “The War Against the Muslims.” In Rebels, Warlords and Ulama: A Reader on Muslim Separatism and the War in Southern Philippines. Ed. Kristina Gaerlan and Mara Stankovitch. Quezon City: Institute for Popular Democracy, pp. 21-37.
Alcala-Hall, Rosalie. 2009. “From Rebels to Soldiers: An Analysis of the Philippine and East Timorese Policy Integrating Former Moro National Liberation Front and Falintil Combatants into the Armed Forces.” Paper presented at the American Political Science Association, Toronto, Canada.
Che Man, W. K. 1990. Muslim Separatism: The Moros of Southern Philippines and the Malays of Southern Thailand. Quezon City: Ateneo de Manila University Press.
Depayso, Yerson (Col.). 2004. “An Assessment of the MNLF Integration Program.” Master’s thesis in National Security Administration, National Defense College of the Philippines.
Fearon, James D. 2004. “Why Do Some Civil Wars Last So Much Longer than Others?” Journal of Peace Research 41(3): 275-301.
Ferrer, Miriam. 2000. “Integration of MNLF Forces into the PNP and AFP: Integration without Demobilization and Disarmament.” UP Project on Assessment of the Implementation of the GRP-MNLF Peace Agreement, Phase I. UP Center for Integrative and Development Studies.
George, T. J. S. 1980. Revolt in Mindanao: The Rise of Islam in Philippine Politics. Kuala Lumpur: Oxford University Press.
GRP-MNLF. 1987. Joint Statements of the Philippine Government and the MNLF Panels (Jeddah Accord). United States Institute of Peace < https://docs.google.com/viewer?url=http%3A%2F%2Fwww.ucd.ie%2Fibis%2Ffilestore%2FJeddah%25201987.pdf> 10 January 2012.
Gutierrez, Eric and Marites Vitug. 1999. “ARMM After the Peace Agreement: An Assessment of Local Government Capability in the Autonomous Region of Muslim Mindanao.” In Rebels, Warlords and Ulama: A Reader on Muslim Separatism and the War in Southern Philippines. Ed. Kristina Gaerlan and Mara Stankovitch. Quezon City: Institute for Popular Democracy, pp.181-221.
Gutierrez, Eric. 1999. “The Problems of Peace.” In Rebels, Warlords and Ulama: A Reader on Muslim Separatism and the War in Southern Philippines. Ed. Kristina Gaerlan and Mara Stankovitch. Quezon City: Institute for Popular Democracy, pp. 223-261.
Human Development Network. 2005. Philippine Human Development Report. Manila: Human Development Network.
Iribani, Abraham. 2006. Give Peace a Chance: The Story of the GRP-MNLF Peace Talks. Mandaluyong City: Magbassa Kita Foundation.
Jacildo, Nerlyne C. 2003. “Experiences of MNLF Integrees in Basilan and Zamboanga: Issues and
Problems”. Unpublished Masters Thesis. University of the Philippines- Diliman. Quezon City.
Jubair, Salah. 1999. Bangsamoro: A Nation Under Endless Tyranny. Kuala Lumpur: IQ Marin Sdn Bhd.
Lara, Francisco Jr. 2010. “Collision and collusion in Muslim Mindanao.” Autonomy and Peace Review 6(1): 84-88.
Majul, Cesar Adib. 1985. The Contemporary Muslim Movement in the Philippines. Berkeley: Mizan Press.
Makinano, Merliza and Alfredo Lubang. 2000. “Disarmament, Demobilization and Reintegration: The Mindanao Experience.” In South Asia at Gunpoint: Small Arms & Light Weapons Proliferation. Ed. Dipankar Banerjee. Colombo, Sri Lanka: Regional Centre for Strategic Studies.
McKenna, Thomas. 1998. Muslim Rulers and Rebels: Everyday Politics and Armed Separatism in the Southern Philippines. Manila: Anvil Publishing , Inc.
Misuari, Nur. 1974. “The Manifesto of the Moro National Liberation Front: Establishment of the Bangsa Moro Republik”. 28 April.
Noble, Lela. 1976. “The Moro National Liberation Front in the Philippines.” Pacific Affairs 49(3): 405-424.
Noble, Leal. 1981. “Muslim Separatism in the Philippines, 1972-1981: The Making of a Stalemate.” Asian Survey 21(11): 1097-1114.
Organization of the Islamic Conference (OIC). 2006. “Report of the Secretary General on the Question of Muslims in Southern Philippines.” OIC/33-ICFM/2005/MM/SG/REP.2). In Reports of the Secretary General on Muslim Minorities and Communities in Non-OIC Member States. Submitted to the 33rd Session of the Islamic Conference of Foreign Ministers, Baku, 19-21 June.
Ramos, Fidel V. 1996. Break Not the Peace: The Story of the GRP-MNLF Peace Negotiations, 1992-1996. Manila: Friends of Steady Eddie.
Rocamora, Joel. 1999. “Dissidence and Development: Perspectives for a Tri-People Approach.” In Rebels, Warlords and Ulama: A Reader on Muslim Separatism and the War in Southern Philippines. Ed. Kristina Gaerlan and Mara Stankovitch. Quezon City: Institute for Popular Democracy, pp. 163-179.
Rodil, B. R. 2000. Kalinaw Mindanaw: The Story of the GRP-MNLF Peace Process. Davao City: Alternate Forum for Research in Mindanao.
Santos, Soliman Jr. (2010a). “War and Peace on the Moro Front: Three Standard Bearers, Three Forms of Struggle, Three Tracks (Overview).” In Primed and Purposeful: Armed Groups and Human Security Efforts in the Philippines. Ed. Diana Rodriguez. Geneva: Small Arms Survey/South-South Network for Non-State Armed Group Engagement, pp. 58-90.
Santos, Soliman Jr. (2010b). “MNLF Integration into the AFP and the PNP: Successful Cooptation or Failed Transformation.” In Primed and Purposeful: Armed Groups and Human Security Efforts in the Philippines. Ed. Diana Rodriguez. Geneva: Small Arms Survey/South-South Network for Non-State Armed Group Engagement, pp. 162-184.
Stedman, Stephen, Donald Rothchild and Elizabeth Cousens. 2002. Ending Civil Wars: The Implementation of Peace Agreements. Lynne Reinner Publishers.
Vitug, Marites and Glenda Gloria. 2000. Under the Crescent Moon: Rebellion in Mindanao. Quezon City: Ateneo Center for Social Policy and Public Affairs and Institute for Popular Democracy.
Weiner, Myron. 1978. Sons of the Soil: Migration and Ethnic Conflict in India. Princeton: Princeton University Press.
 As vice president of the National Defense College of the Philippines (NDCP) in the late 1990s, I participated in the vetting of these MNLF commanders and fighters. The latter wanted to be commissioned as officers of the Armed Forces of the Philippines (AFP) or the Philippine National Police (PNP). However, they could not all be accommodated since most of them were illiterate and nearing the mandatory retirement age.